Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:01 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for biodbLipidmaps on nebbiolo1


To the developers/maintainers of the biodbLipidmaps package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

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

Summary

Package: biodbLipidmaps
Version: 1.2.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings biodbLipidmaps_1.2.0.tar.gz
StartedAt: 2022-10-18 18:46:28 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 18:49:28 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 180.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings biodbLipidmaps_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2022-10-18 18:47:11.799][biodb::testContext]
biodb.INFO [2022-10-18 18:47:11.802][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:47:11.803][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-10-18 18:47:11.804][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:47:11.805][biodb::testContext]
biodb.INFO [2022-10-18 18:47:11.825][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:47:11.827][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 18:47:11.836][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:11.837][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 18:47:11.839][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 18:47:11.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.843][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 18:47:11.886][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 18:47:11.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.890][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 18:47:11.891][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 18:47:11.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.894][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 18:47:11.896][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 18:47:11.897][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 18:47:11.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.900][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 18:47:11.901][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 18:47:11.902][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 18:47:11.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.906][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 18:47:11.907][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 18:47:11.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.911][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 18:47:11.912][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 18:47:11.913][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 18:47:11.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.916][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 18:47:11.917][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 18:47:11.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.921][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 18:47:11.922][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 18:47:11.923][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 18:47:11.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.926][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:47:11.927][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 18:47:11.928][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 18:47:11.929][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 18:47:11.930][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 18:47:11.931][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 18:47:11.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.935][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 18:47:11.936][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 18:47:11.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.939][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 18:47:11.940][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 18:47:11.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.944][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 18:47:11.945][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 18:47:11.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.949][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 18:47:11.949][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 18:47:11.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.953][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 18:47:11.954][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 18:47:11.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.957][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:47:11.958][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 18:47:11.963][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 18:47:11.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.967][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 18:47:11.968][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 18:47:11.969][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 18:47:11.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:11.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:11.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:11.975][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 18:47:12.006][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.019][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 18:47:12.020][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.021][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:12.022][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.023][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.024][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.025][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.026][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:47:12.027][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:12.028][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.029][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 18:47:12.030][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:12.031][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.031][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.032][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:12.032][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:47:12.032][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:47:12.032][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:47:12.032][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:47:12.033][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:12.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:12.035][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:12.036][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:12.037][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:12.038][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:12.038][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.039][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.040][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:12.041][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:12.042][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.043][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.044][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 18:47:12.046][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.047][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:47:12.048][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.049][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:12.050][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.051][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.051][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.052][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.059][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:47:12.060][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:12.061][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.062][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 18:47:12.063][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:12.063][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.064][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.065][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:12.065][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:47:12.065][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:47:12.065][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:47:12.065][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:47:12.066][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:12.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:12.068][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:12.069][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:12.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:12.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:12.071][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.072][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.073][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:12.074][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:12.075][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.076][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.077][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 18:47:12.079][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.080][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 18:47:12.081][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.082][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:12.083][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.084][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.084][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.085][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.086][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:47:12.087][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:12.088][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.089][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 18:47:12.090][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:12.091][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.092][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.093][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.094][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:12.095][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:12.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:12.096][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:12.097][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:12.098][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:12.099][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.100][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.101][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:12.102][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:12.103][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.104][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.105][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 18:47:12.106][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.107][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:47:12.108][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.109][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:12.110][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.111][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.112][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.113][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.114][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:47:12.115][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:12.116][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.117][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 18:47:12.118][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:12.119][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.120][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.121][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.122][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:12.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:12.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:12.125][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:12.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:12.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:12.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.128][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.129][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:12.130][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:12.131][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.132][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.136][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:12.137][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.138][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[2022-10-18 18:47:12.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.142][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[2022-10-18 18:47:12.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.160][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[2022-10-18 18:47:12.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.164][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[2022-10-18 18:47:12.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.169][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[2022-10-18 18:47:12.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.173][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[2022-10-18 18:47:12.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.182][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[2022-10-18 18:47:12.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.214][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 18:47:12.219][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 18:47:12.220][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 18:47:12.221][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 18:47:12.223][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:47:12.224][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:47:12.225][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 18:47:12.227][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 18:47:12.228][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 18:47:12.229][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:47:12.230][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:47:12.232][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 18:47:12.233][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 18:47:12.234][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 18:47:12.236][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 18:47:12.237][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:47:12.238][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 18:47:12.244][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 18:47:12.246][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:47:12.247][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 18:47:12.248][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 18:47:12.249][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 18:47:12.251][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 18:47:12.252][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 18:47:12.253][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 18:47:12.254][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 18:47:12.256][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 18:47:12.257][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 18:47:12.258][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 18:47:12.260][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 18:47:12.261][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 18:47:12.262][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 18:47:12.264][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 18:47:12.265][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 18:47:12.266][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 18:47:12.268][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 18:47:12.269][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 18:47:12.270][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 18:47:12.271][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 18:47:12.273][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 18:47:12.274][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 18:47:12.275][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 18:47:12.277][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 18:47:12.278][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 18:47:12.279][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 18:47:12.281][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 18:47:12.282][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 18:47:12.283][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 18:47:12.285][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 18:47:12.286][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 18:47:12.287][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 18:47:12.289][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 18:47:12.290][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 18:47:12.291][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 18:47:12.293][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 18:47:12.294][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 18:47:12.295][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 18:47:12.297][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 18:47:12.298][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 18:47:12.299][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 18:47:12.300][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 18:47:12.302][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 18:47:12.303][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 18:47:12.304][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 18:47:12.306][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 18:47:12.307][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 18:47:12.308][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:47:12.310][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:47:12.311][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 18:47:12.312][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 18:47:12.314][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 18:47:12.315][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 18:47:12.316][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 18:47:12.318][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 18:47:12.319][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 18:47:12.320][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 18:47:12.321][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 18:47:12.323][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 18:47:12.324][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 18:47:12.326][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 18:47:12.327][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 18:47:12.328][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 18:47:12.330][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 18:47:12.335][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 18:47:12.337][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:47:12.340][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:47:12.341][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.343][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:47:12.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:12.458][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-10-18 18:47:12.475][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 18:47:12.478][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.480][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.482][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.483][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:47:12.485][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.487][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.488][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.489][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.491][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:47:12.493][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:47:12.494][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.496][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-10-18 18:47:12.497][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:47:12.498][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-10-18 18:47:12.498][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-10-18 18:47:12.498][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-10-18 18:47:12.498][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-10-18 18:47:12.498][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-10-18 18:47:12.498][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-10-18 18:47:12.498][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-10-18 18:47:12.498][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-10-18 18:47:12.498][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-10-18 18:47:12.500][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 18:47:12.500][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:47:12.500][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:47:12.501][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:47:12.502][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:12.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:12.504][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:47:12.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:47:12.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:47:12.507][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:47:12.509][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 18:47:12.509][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-10-18 18:47:12.510][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:47:12.510][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:47:12.511][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 18:47:12.512][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:47:12.519][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-10-18 18:47:12.520][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:47:12.550][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 18:47:12.552][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-10-18 18:47:12.557][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 18:47:12.562][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-10-18 18:47:12.566][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 18:47:12.568][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 18:47:12.569][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-10-18 18:47:12.570][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-10-18 18:47:12.587][biodb::testThat]
biodb.INFO [2022-10-18 18:47:12.588][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2022-10-18 18:47:12.589][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:12.590][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:12.594][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.15-bioc/R/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2022-10-18 18:47:12.599][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:12.603][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 18:47:12.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:12.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:12.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:12.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:12.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:12.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:12.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:12.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:12.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:12.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:12.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:12.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:12.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:12.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.715][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:12.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:12.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.719][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:12.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:12.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.723][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:12.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:12.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.748][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:12.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:12.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.756][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:12.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:12.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.760][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:12.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:12.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.766][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:47:12.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:12.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.770][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:47:12.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:12.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.777][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:12.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:12.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.781][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:12.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:12.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:12.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:12.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:12.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:12.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.798][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:47:12.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:12.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.802][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 18:47:12.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:12.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:12.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:12.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:12.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:12.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.814][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:47:12.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:12.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:12.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:12.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.844][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:12.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:12.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:12.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:12.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:12.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:12.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.884][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:12.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:12.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.891][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:12.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:12.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.895][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:12.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:12.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:12.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:12.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.903][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:12.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:12.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:12.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:12.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:12.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:12.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:12.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:12.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:12.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:12.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:12.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:12.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:12.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:12.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:12.934][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2022-10-18 18:47:12.939][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:12.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:12.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.943][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:12.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:12.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.947][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:12.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:12.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.951][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:12.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:12.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:12.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:12.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:12.994][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:12.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:12.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:12.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.032][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:13.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:13.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.036][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:13.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:13.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.040][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:13.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:13.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.070][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.071][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.071][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.072][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.096][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.097][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.098][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.099][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.111][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.115][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.123][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.124][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.125][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.126][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.127][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.143][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:13.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:13.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.147][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:13.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:13.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.151][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:13.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:13.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.155][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:13.156][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:13.157][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.158][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.159][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:13.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:13.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.181][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.183][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.183][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.184][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.196][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.200][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.204][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.208][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.209][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.210][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.211][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.212][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.222][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.224][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.225][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.225][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.230][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.231][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.232][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.233][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.238][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:13.239][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:13.240][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.241][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.246][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.247][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.248][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.249][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.254][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.255][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.256][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.257][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.262][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.263][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.264][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.265][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:13.271][biodb::testThat]
biodb.INFO [2022-10-18 18:47:13.272][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-10-18 18:47:13.273][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:13.274][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:13.292][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2022-10-18 18:47:13.300][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:47:13.304][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2022-10-18 18:47:13.305][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:13.307][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2022-10-18 18:47:13.308][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:13.352][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:47:13.353][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 18:47:13.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:13.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:13.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:13.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:13.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:13.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:13.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:13.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:13.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:13.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:13.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:13.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.392][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:13.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:13.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.397][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:13.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:13.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.401][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.405][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:13.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.413][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.418][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:13.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.426][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:47:13.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.430][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:47:13.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:13.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.438][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:13.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:13.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.443][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:13.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:13.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.472][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:47:13.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.476][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 18:47:13.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.484][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.488][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:47:13.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.505][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.520][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:13.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:13.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.524][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:13.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:13.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.532][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:13.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:13.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:13.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:13.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:13.566][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2022-10-18 18:47:13.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-10-18 18:47:13.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-10-18 18:47:13.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-10-18 18:47:13.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-10-18 18:47:13.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-10-18 18:47:13.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-10-18 18:47:13.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:13.586][biodb::testThat]
biodb.INFO [2022-10-18 18:47:13.587][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2022-10-18 18:47:13.588][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:13.589][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:13.592][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.594][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.595][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.596][ef$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:13.597][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2022-10-18 18:47:13.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:13.639][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:13.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:13.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:13.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:13.644][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 18:47:13.791][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 18:47:13.811][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:13.812][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:13.814][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2022-10-18 18:47:15.109][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2022-10-18 18:47:16.107][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:16.115][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2022-10-18 18:47:16.145][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2022-10-18 18:47:16.150][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2022-10-18 18:47:16.162][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:16.164][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:16.165][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.166][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:16.168][biodb::testThat]
biodb.INFO [2022-10-18 18:47:16.169][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2022-10-18 18:47:16.169][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:16.170][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:16.199][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:16.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:16.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:16.203][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:16.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:16.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:16.207][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:16.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:16.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:16.329][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 18:47:16.333][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:16.347][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-10-18 18:47:16.348][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:16.350][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2022-10-18 18:47:16.364][biodb::testThat]
biodb.INFO [2022-10-18 18:47:16.365][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2022-10-18 18:47:16.366][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:16.367][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:16.391][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:16.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:16.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:16.396][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:16.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:16.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:16.400][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:16.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:16.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:16.404][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:16.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:16.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:16.453][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:16.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:16.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:16.458][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:47:16.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:47:16.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:16.462][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:16.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 18:47:16.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:16.465][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:16.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 18:47:16.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:16.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:16.472][biodb::testThat]
biodb.INFO [2022-10-18 18:47:16.473][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-10-18 18:47:16.474][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:16.474][biodb::testThat]
biodb.INFO [2022-10-18 18:47:16.479][biodb::testThat]
biodb.INFO [2022-10-18 18:47:16.480][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-10-18 18:47:16.481][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:16.482][biodb::testThat]
biodb.INFO [2022-10-18 18:47:16.486][biodb::testThat]
biodb.INFO [2022-10-18 18:47:16.487][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2022-10-18 18:47:16.488][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:16.489][biodb::testThat]
biodb.DEBUG[2022-10-18 18:47:16.493][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2022-10-18 18:47:17.243][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2022-10-18 18:47:17.670][biodb::testThat]
biodb.INFO [2022-10-18 18:47:17.672][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2022-10-18 18:47:17.673][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:17.673][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:17.683][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:17.684][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:17.685][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:17.686][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:17.687][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:17.688][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:17.689][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:17.690][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:17.691][biodb::testThat]
biodb.INFO [2022-10-18 18:47:17.692][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2022-10-18 18:47:17.693][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:17.694][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:17.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:17.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:17.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:17.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:17.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:17.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:17.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:17.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:17.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:17.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:17.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:17.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:17.937][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 18:47:17.940][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:17.942][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-10-18 18:47:17.943][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:17.945][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2022-10-18 18:47:18.159][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 18:47:18.173][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:47:18.177][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-10-18 18:47:18.181][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:47:18.184][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2022-10-18 18:47:18.230][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:18.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:18.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:18.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:18.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:18.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:18.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:18.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:18.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:18.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:18.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:18.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:18.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:18.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:18.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:18.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:18.436][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2022-10-18 18:47:18.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:18.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:18.472][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2022-10-18 18:47:23.984][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2022-10-18 18:47:34.495][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2022-10-18 18:47:34.501][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2022-10-18 18:47:34.507][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2022-10-18 18:47:34.535][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2022-10-18 18:47:35.142][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2022-10-18 18:47:35.148][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:35.150][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:35.154][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2022-10-18 18:47:36.088][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2022-10-18 18:47:36.833][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:36.850][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2022-10-18 18:47:36.870][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2022-10-18 18:47:36.965][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2022-10-18 18:47:36.969][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:36.970][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:36.973][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2022-10-18 18:47:37.619][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2022-10-18 18:47:38.269][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:38.281][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2022-10-18 18:47:38.397][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2022-10-18 18:47:38.426][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 18:47:38.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 18:47:38.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:38.448][biodb::testThat]
biodb.INFO [2022-10-18 18:47:38.450][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2022-10-18 18:47:38.451][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:38.453][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:38.458][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:38.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:38.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:38.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:38.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:38.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:38.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:38.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:38.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:38.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:38.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:38.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:38.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:38.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:38.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:38.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:38.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:38.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:38.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:38.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:38.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:38.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:38.651][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2022-10-18 18:47:38.655][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:38.656][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:38.658][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2022-10-18 18:47:44.219][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2022-10-18 18:47:54.345][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2022-10-18 18:47:54.354][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2022-10-18 18:47:54.361][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2022-10-18 18:47:54.395][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2022-10-18 18:47:54.736][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2022-10-18 18:47:54.784][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-10-18 18:47:54.786][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2022-10-18 18:47:54.788][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-10-18 18:47:54.789][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:47:54.790][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:47:54.791][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 18:47:54.792][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:47:54.793][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:47:54.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:54.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:54.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:54.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:54.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:54.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:54.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:54.822][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2022-10-18 18:47:54.825][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:54.826][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:54.828][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2022-10-18 18:47:55.479][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2022-10-18 18:47:56.187][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:56.194][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2022-10-18 18:47:56.205][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2022-10-18 18:47:56.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:56.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:56.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:56.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:56.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:56.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:56.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:56.221][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2022-10-18 18:47:56.223][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:56.224][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:56.225][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2022-10-18 18:47:56.870][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2022-10-18 18:47:57.506][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:47:57.513][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2022-10-18 18:47:57.524][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2022-10-18 18:47:57.533][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2022-10-18 18:47:57.537][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:47:57.578][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-10-18 18:47:57.579][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 18:47:57.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:57.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:57.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:57.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:57.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:57.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:57.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:57.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:57.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:57.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:57.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:57.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.615][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:57.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:57.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.618][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:57.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:57.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.622][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:57.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:57.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.626][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:57.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:57.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.633][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:57.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:57.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.636][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:57.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:57.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.643][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:47:57.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:57.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.647][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:47:57.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:57.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.653][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:57.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:57.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.657][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:57.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:57.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.664][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:57.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:57.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.674][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:47:57.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.678][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 18:47:57.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.682][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:57.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:57.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.689][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:47:57.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.696][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.700][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.708][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:57.726][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:57.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:57.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:57.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:57.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:57.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:57.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:57.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:47:57.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:47:57.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.753][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:57.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:47:57.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.757][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:57.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:47:57.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.761][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:57.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:57.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.765][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:57.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:47:57.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.772][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:57.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:57.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.776][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:57.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:47:57.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.782][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:47:57.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:57.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.786][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:47:57.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:57.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.793][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:57.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:57.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.797][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:47:57.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:47:57.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:57.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:57.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.815][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:47:57.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.819][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 18:47:57.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.823][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:57.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.827][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:47:57.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.830][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:47:57.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:47:57.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.837][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.841][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.849][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:47:57.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:47:57.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:57.902][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2022-10-18 18:47:57.911][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 18:47:57.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:57.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:57.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:57.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:57.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:57.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:57.921][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[2022-10-18 18:47:57.923][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.926][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.930][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:47:57.931][private$selectFields]
biodb.TRACE[2022-10-18 18:47:57.932][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:57.933][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:57.934][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:47:57.935][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.936][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.937][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.937][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.938][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.939][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.940][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.941][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.942][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:47:57.943][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:47:57.944][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.945][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.946][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.947][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.948][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 18:47:57.949][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.953][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.957][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.970][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-10-18 18:47:57.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:57.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:57.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:57.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:57.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:57.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:57.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:47:57.981][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.985][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.989][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:47:57.990][private$selectFields]
biodb.TRACE[2022-10-18 18:47:57.990][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:57.991][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:57.992][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:47:57.993][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.995][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.995][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:57.996][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:57.997][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.998][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:57.999][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.000][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.001][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:47:58.002][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:47:58.003][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.004][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.005][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.005][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.006][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 18:47:58.007][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.011][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.015][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.019][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-10-18 18:47:58.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:58.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:58.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:58.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:58.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:58.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:58.030][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[2022-10-18 18:47:58.031][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.035][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.039][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:47:58.040][private$selectFields]
biodb.TRACE[2022-10-18 18:47:58.041][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:47:58.041][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:47:58.042][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:47:58.043][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.044][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.045][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.046][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.047][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.048][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.049][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.050][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.050][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:47:58.051][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:47:58.052][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.053][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.054][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.055][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.056][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 18:47:58.057][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.061][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.065][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:47:58.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.069][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-10-18 18:47:58.070][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 18:47:58.071][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 18:47:58.080][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 18:47:58.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 18:47:58.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:47:58.086][biodb::testThat]
biodb.INFO [2022-10-18 18:47:58.087][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2022-10-18 18:47:58.088][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:47:58.089][biodb::testThat]
biodb.TRACE[2022-10-18 18:47:58.092][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:47:58.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:47:58.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:58.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:47:58.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:58.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:58.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:58.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:58.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:58.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:58.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:47:58.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:58.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:47:58.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:47:58.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:47:58.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:47:58.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:47:58.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:47:58.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:47:58.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:47:58.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:47:58.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:47:58.309][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2022-10-18 18:47:58.313][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:47:58.315][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:47:58.317][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2022-10-18 18:48:04.453][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2022-10-18 18:48:16.256][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:48:16.266][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2022-10-18 18:48:16.293][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2022-10-18 18:48:16.664][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 18:48:16.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:16.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:16.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:16.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:16.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:16.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:16.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:48:16.725][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.733][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.762][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:16.764][private$selectFields]
biodb.TRACE[2022-10-18 18:48:16.765][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:48:16.766][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:48:16.768][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:16.769][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.770][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.771][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.772][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.773][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.774][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.775][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.776][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.777][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:16.789][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:16.790][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.791][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.792][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.793][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.794][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 18:48:16.796][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.800][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.804][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.809][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-10-18 18:48:16.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:16.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:16.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:16.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:16.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:16.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:16.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:48:16.822][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.826][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.830][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:16.831][private$selectFields]
biodb.TRACE[2022-10-18 18:48:16.832][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:48:16.833][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:48:16.834][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:16.835][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.836][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.837][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.838][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.840][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.841][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.842][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.843][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.844][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:16.845][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:16.846][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.847][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.848][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.849][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.850][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 18:48:16.851][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.855][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.859][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.864][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-10-18 18:48:16.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:16.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:16.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:16.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:16.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:16.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:16.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:48:16.878][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.882][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.886][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:16.887][private$selectFields]
biodb.TRACE[2022-10-18 18:48:16.888][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:48:16.889][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:48:16.890][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:16.891][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.893][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.894][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.895][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.896][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.897][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.898][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.899][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.900][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:16.901][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:16.902][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.903][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.904][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.905][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.906][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 18:48:16.907][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.911][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.916][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:16.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.940][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-10-18 18:48:16.941][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 18:48:16.942][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 18:48:16.950][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 18:48:16.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 18:48:16.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:48:16.957][biodb::testThat]
biodb.INFO [2022-10-18 18:48:16.958][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2022-10-18 18:48:16.959][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:16.960][biodb::testThat]
biodb.TRACE[2022-10-18 18:48:16.963][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 18:48:16.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 18:48:16.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 18:48:16.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 18:48:16.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:16.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:16.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:16.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:16.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:16.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:16.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:16.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:16.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:16.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:16.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:48:16.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:16.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:17.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:17.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:17.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:17.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:17.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:17.135][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2022-10-18 18:48:17.139][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:48:17.141][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2022-10-18 18:48:17.142][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:48:17.193][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2022-10-18 18:48:17.785][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 18:48:17.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:17.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:17.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:17.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:17.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:17.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:17.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:48:17.798][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.803][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.807][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:17.808][private$selectFields]
biodb.TRACE[2022-10-18 18:48:17.808][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:48:17.809][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:48:17.810][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:17.811][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.813][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.814][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.815][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.816][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.817][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.818][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.819][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.820][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:17.821][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:17.821][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.822][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.823][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.824][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.825][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 18:48:17.826][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.830][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.834][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.838][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-10-18 18:48:17.839][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:17.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:17.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:17.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:17.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:17.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:17.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:48:17.851][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.855][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.859][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:17.860][private$selectFields]
biodb.TRACE[2022-10-18 18:48:17.861][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:48:17.862][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:48:17.862][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:17.863][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.864][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.865][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.867][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.868][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.869][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.870][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.871][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.872][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:17.873][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:17.895][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.896][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.897][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.898][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.899][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 18:48:17.900][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.904][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.908][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.912][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-10-18 18:48:17.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:17.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:17.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:17.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:17.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:17.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:17.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:48:17.925][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.929][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.933][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:17.934][private$selectFields]
biodb.TRACE[2022-10-18 18:48:17.935][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 18:48:17.935][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:48:17.936][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:17.937][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.938][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.939][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.940][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.941][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.942][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.943][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.944][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.945][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:17.946][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:48:17.947][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.948][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.949][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.950][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.951][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 18:48:17.952][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.956][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.960][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:17.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:17.965][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-10-18 18:48:17.966][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 18:48:17.967][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 18:48:17.989][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 18:48:17.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 18:48:17.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:17.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 18:48:17.996][biodb::testThat]
biodb.INFO [2022-10-18 18:48:17.997][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2022-10-18 18:48:17.998][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:17.999][biodb::testThat]
biodb.DEBUG[2022-10-18 18:48:18.001][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-10-18 18:48:18.002][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 18:48:18.004][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-10-18 18:48:18.005][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 18:48:18.007][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:48:18.008][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:48:18.009][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 18:48:18.010][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:48:18.011][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:48:18.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:18.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:18.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:18.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:18.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:18.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:18.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:18.039][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2022-10-18 18:48:18.042][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:18.043][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:18.045][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 18:48:18.673][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:18.675][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:18.677][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:18.679][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 18:48:19.402][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:19.403][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:19.404][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:19.405][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 18:48:19.947][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:19.950][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:19.952][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:19.953][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 18:48:20.778][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:20.779][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:20.780][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:20.782][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 18:48:21.387][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:21.389][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:21.391][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:21.393][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 18:48:22.173][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:22.176][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:22.178][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:22.180][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 18:48:22.783][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:22.785][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:22.787][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:22.789][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 18:48:23.616][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:23.617][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:23.619][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:23.621][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 18:48:24.252][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:24.255][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:24.257][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:24.258][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 18:48:25.086][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:25.088][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:25.090][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:25.092][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 18:48:25.708][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:25.710][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:25.712][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:25.714][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 18:48:26.544][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:26.546][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:26.548][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:26.551][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 18:48:27.167][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:27.170][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:27.172][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:27.175][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 18:48:27.952][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:27.954][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:27.956][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:27.958][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 18:48:28.575][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:28.577][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:28.579][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:28.581][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 18:48:29.408][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:29.410][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:29.412][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:29.414][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 18:48:30.020][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:30.022][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:30.024][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:30.026][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 18:48:30.746][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:30.748][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:30.749][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:30.750][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 18:48:31.353][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:31.356][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:31.359][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:31.361][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 18:48:32.189][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2022-10-18 18:48:32.203][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2022-10-18 18:48:32.212][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:48:32.257][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-10-18 18:48:32.261][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 18:48:32.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:32.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:32.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:32.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:32.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:32.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:32.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:48:32.291][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:32.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:32.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:32.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:32.299][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:32.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:32.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:32.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:32.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:32.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:32.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:32.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:32.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:32.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:32.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:32.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:32.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:32.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:32.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:32.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:32.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:32.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:32.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:32.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:32.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:32.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:32.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:32.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:32.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:32.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:32.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:32.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:48:32.345][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2022-10-18 18:48:32.347][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2022-10-18 18:48:32.361][biodb::testThat]
biodb.INFO [2022-10-18 18:48:32.363][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2022-10-18 18:48:32.365][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:32.367][biodb::testThat]
biodb.DEBUG[2022-10-18 18:48:32.383][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2022-10-18 18:48:32.386][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2022-10-18 18:48:32.389][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-10-18 18:48:32.455][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2022-10-18 18:48:32.458][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-10-18 18:48:32.460][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 18:48:32.462][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:48:32.464][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 18:48:32.467][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:48:32.468][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:48:32.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:32.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:32.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:32.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:32.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:32.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:32.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:32.500][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2022-10-18 18:48:32.506][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:32.508][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:32.509][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 18:48:33.122][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:33.125][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:33.128][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:33.129][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 18:48:33.862][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:33.865][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:33.867][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:33.869][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 18:48:34.490][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:34.493][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:34.496][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:34.498][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 18:48:35.333][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:35.336][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:35.339][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:35.342][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 18:48:35.966][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:35.968][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:35.970][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:35.972][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 18:48:36.703][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:36.706][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:36.708][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:36.710][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 18:48:37.324][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:37.327][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:37.330][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:37.332][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 18:48:38.164][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:38.166][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:38.168][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:38.171][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 18:48:38.792][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:38.794][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:38.796][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:38.797][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 18:48:39.627][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:39.629][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:39.631][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:39.633][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 18:48:40.254][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:40.256][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:40.259][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:40.261][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 18:48:41.085][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:41.087][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:41.089][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:41.091][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 18:48:41.717][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:41.719][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:41.721][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:41.723][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 18:48:42.549][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:42.551][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:42.552][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:42.554][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 18:48:43.170][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:43.173][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:43.175][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:43.178][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 18:48:43.995][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:43.996][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:43.998][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:44.000][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 18:48:44.616][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:44.618][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:44.620][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:44.622][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 18:48:45.452][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:45.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:45.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:45.458][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 18:48:46.079][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 18:48:46.081][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 18:48:46.084][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 18:48:46.086][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 18:48:46.818][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 18:48:46.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:46.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:46.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:46.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:46.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:46.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:46.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:48:46.840][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2022-10-18 18:48:46.844][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:46.846][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:46.848][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2022-10-18 18:48:47.506][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2022-10-18 18:48:48.194][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:48:48.208][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2022-10-18 18:48:48.234][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2022-10-18 18:48:48.253][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2022-10-18 18:48:48.261][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:48:48.288][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-10-18 18:48:48.291][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 18:48:48.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:48.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:48.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:48.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:48.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:48.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:48.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:48:48.315][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:48.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:48.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.322][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:48.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:48.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:48:48.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:48:48.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:48:48.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:48:48.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:48:48.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:48:48.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:48:48.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:48:48.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:48.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:48.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:48:48.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:48:48.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.396][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:48:48.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:48:48.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.400][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:48:48.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:48:48.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.408][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:48.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:48.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.413][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:48.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:48:48.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.421][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:48:48.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:48:48.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.425][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:48:48.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:48:48.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.434][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:48:48.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:48:48.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.439][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:48:48.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:48:48.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.485][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:48:48.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:48.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.490][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:48:48.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:48:48.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:48:48.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:48:48.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.504][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:48:48.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:48:48.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.512][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:48.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:48.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.516][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:48.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:48.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.524][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:48:48.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:48.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.529][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 18:48:48.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:48.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:48.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:48.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:48.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:48.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.542][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:48:48.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:48.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:48.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:48.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:48.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:48.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.558][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:48.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:48.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:48.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:48.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.567][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:48:48.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:48:48.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.574][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:48.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:48.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.579][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:48.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:48.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.588][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:48.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:48:48.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:48:48.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:48:48.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:48:48.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:48:48.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:48:48.643][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2022-10-18 18:48:48.644][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2022-10-18 18:48:48.645][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2022-10-18 18:48:48.657][biodb::testThat]
biodb.INFO [2022-10-18 18:48:48.658][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2022-10-18 18:48:48.659][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:48.660][biodb::testThat]
biodb.INFO [2022-10-18 18:48:48.682][biodb::testThat]
biodb.INFO [2022-10-18 18:48:48.683][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2022-10-18 18:48:48.684][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:48.685][biodb::testThat]
biodb.INFO [2022-10-18 18:48:48.692][biodb::testThat]
biodb.INFO [2022-10-18 18:48:48.693][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2022-10-18 18:48:48.694][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:48:48.695][biodb::testThat]
biodb.DEBUG[2022-10-18 18:48:48.772][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2022-10-18 18:48:48.775][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:48:48.776][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:48:48.778][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2022-10-18 18:48:53.528][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2022-10-18 18:49:03.817][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:49:03.827][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2022-10-18 18:49:03.852][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2022-10-18 18:49:04.496][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:04.497][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:04.498][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:04.499][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:04.500][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:04.501][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:04.502][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:04.503][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 18:49:04.505][biodb::testThat]
biodb.INFO [2022-10-18 18:49:04.506][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2022-10-18 18:49:04.507][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:49:04.507][biodb::testThat]
biodb.ERROR[2022-10-18 18:49:04.521][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2022-10-18 18:49:04.537][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2022-10-18 18:49:04.547][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 18:49:04.548][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-10-18 18:49:04.550][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-10-18 18:49:04.551][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 18:49:04.551][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:04.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:04.553][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.555][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 18:49:04.566][biodb::testContext]
biodb.INFO [2022-10-18 18:49:04.568][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:49:04.569][biodb::testContext] Test context - Web services tests
biodb.INFO [2022-10-18 18:49:04.570][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:49:04.571][biodb::testContext]
biodb.INFO [2022-10-18 18:49:04.577][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:49:04.579][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 18:49:04.583][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:49:04.585][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 18:49:04.586][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 18:49:04.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.590][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 18:49:04.591][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 18:49:04.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.594][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 18:49:04.595][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 18:49:04.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.599][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 18:49:04.600][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 18:49:04.601][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 18:49:04.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.605][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 18:49:04.606][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 18:49:04.607][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 18:49:04.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.610][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 18:49:04.611][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 18:49:04.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.615][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 18:49:04.616][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 18:49:04.617][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 18:49:04.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.620][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 18:49:04.621][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 18:49:04.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.625][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 18:49:04.626][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 18:49:04.627][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 18:49:04.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.630][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:49:04.631][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 18:49:04.632][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 18:49:04.633][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 18:49:04.634][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 18:49:04.635][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 18:49:04.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.639][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 18:49:04.640][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 18:49:04.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.643][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 18:49:04.644][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 18:49:04.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.648][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 18:49:04.649][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 18:49:04.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.652][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[2022-10-18 18:49:04.653][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 18:49:04.654][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 18:49:04.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.657][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 18:49:04.658][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 18:49:04.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.662][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:49:04.663][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 18:49:04.668][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 18:49:04.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.672][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 18:49:04.673][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 18:49:04.674][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 18:49:04.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.678][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 18:49:04.680][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:04.681][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 18:49:04.682][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.683][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:49:04.684][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.685][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:49:04.686][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:04.687][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:49:04.688][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:49:04.689][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:49:04.690][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.691][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 18:49:04.692][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:49:04.693][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.694][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.695][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:49:04.695][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:49:04.695][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:49:04.695][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:49:04.695][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:49:04.696][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:49:04.697][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:04.697][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:04.698][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:49:04.699][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:04.700][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:04.701][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:49:04.702][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.703][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:49:04.704][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:49:04.705][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:04.706][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.707][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 18:49:04.709][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:04.710][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:49:04.711][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.712][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:49:04.713][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.714][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:49:04.715][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:04.716][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:49:04.717][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:49:04.718][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:49:04.719][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.720][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 18:49:04.721][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:49:04.722][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.723][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.724][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:49:04.724][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:49:04.724][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:49:04.724][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:49:04.724][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:49:04.725][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:49:04.726][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:04.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:04.727][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:49:04.728][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:04.729][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:04.730][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:49:04.731][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.732][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:49:04.733][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:49:04.734][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:04.735][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.736][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 18:49:04.738][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.739][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 18:49:04.740][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.741][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:49:04.742][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.743][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:49:04.744][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:04.745][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:49:04.746][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:49:04.747][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:49:04.748][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:04.749][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 18:49:04.750][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:49:04.751][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.752][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.753][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.754][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:49:04.755][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:04.756][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:04.757][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:49:04.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:04.758][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:04.759][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:49:04.760][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.761][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:49:04.762][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:49:04.763][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:04.764][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.765][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 18:49:04.767][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.768][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:49:04.769][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.770][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:49:04.771][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.772][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:49:04.773][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:04.774][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:49:04.775][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:49:04.776][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:49:04.777][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:04.778][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 18:49:04.779][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:49:04.780][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.781][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:04.782][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.798][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:49:04.800][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:04.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:04.802][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:49:04.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:04.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:04.805][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:49:04.806][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.807][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:49:04.807][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:49:04.808][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:04.809][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:04.811][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:49:04.811][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:04.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:04.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:04.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:04.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:04.888][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 18:49:04.890][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 18:49:04.891][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 18:49:04.893][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 18:49:04.894][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:49:04.895][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:49:04.897][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 18:49:04.898][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 18:49:04.899][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 18:49:04.901][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:49:04.902][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:49:04.903][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 18:49:04.905][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 18:49:04.906][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 18:49:04.907][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 18:49:04.909][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:49:04.910][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 18:49:04.911][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 18:49:04.913][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:49:04.914][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 18:49:04.915][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 18:49:04.917][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 18:49:04.918][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 18:49:04.920][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 18:49:04.921][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 18:49:04.922][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 18:49:04.924][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 18:49:04.925][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 18:49:04.927][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 18:49:04.928][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 18:49:04.929][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 18:49:04.931][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 18:49:04.932][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 18:49:04.934][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 18:49:04.935][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 18:49:04.936][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 18:49:04.938][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 18:49:04.939][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 18:49:04.940][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 18:49:04.942][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 18:49:04.943][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 18:49:04.945][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 18:49:04.946][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 18:49:04.947][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 18:49:04.949][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 18:49:04.950][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 18:49:04.952][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 18:49:04.953][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 18:49:04.954][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 18:49:04.956][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 18:49:04.957][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 18:49:04.958][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 18:49:04.960][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 18:49:04.961][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 18:49:04.963][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 18:49:04.964][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 18:49:04.965][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 18:49:04.967][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 18:49:04.968][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 18:49:04.969][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 18:49:04.971][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 18:49:04.972][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 18:49:04.973][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 18:49:04.975][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 18:49:04.976][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 18:49:04.977][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 18:49:04.980][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:49:04.981][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:49:04.983][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 18:49:04.984][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 18:49:04.986][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 18:49:04.987][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 18:49:04.988][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 18:49:04.990][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 18:49:04.991][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 18:49:04.992][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 18:49:04.994][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 18:49:04.995][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 18:49:04.997][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 18:49:04.998][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 18:49:04.999][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 18:49:05.001][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 18:49:05.002][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 18:49:05.004][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 18:49:05.005][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:49:05.006][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:49:05.007][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.009][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.029][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[2022-10-18 18:49:05.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.041][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[2022-10-18 18:49:05.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.073][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[2022-10-18 18:49:05.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.116][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[2022-10-18 18:49:05.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.123][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[2022-10-18 18:49:05.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:05.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:05.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:05.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:05.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:05.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:05.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:05.136][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-10-18 18:49:05.138][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 18:49:05.140][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:05.141][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 18:49:05.142][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:05.143][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:49:05.144][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:05.145][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:49:05.146][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:05.147][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:49:05.148][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:49:05.149][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:49:05.150][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:05.151][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-10-18 18:49:05.152][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:49:05.153][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-10-18 18:49:05.153][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-10-18 18:49:05.153][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-10-18 18:49:05.153][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-10-18 18:49:05.153][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-10-18 18:49:05.153][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-10-18 18:49:05.153][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-10-18 18:49:05.153][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-10-18 18:49:05.153][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-10-18 18:49:05.154][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:05.155][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:49:05.155][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:49:05.156][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:49:05.157][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:05.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:05.158][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:49:05.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:05.160][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:05.161][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:49:05.162][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 18:49:05.162][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-10-18 18:49:05.163][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:49:05.164][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:49:05.165][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:05.166][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:05.167][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-10-18 18:49:05.168][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:49:05.171][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 18:49:05.172][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-10-18 18:49:05.174][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 18:49:05.175][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-10-18 18:49:05.176][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 18:49:05.177][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 18:49:05.179][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-10-18 18:49:05.180][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-10-18 18:49:05.181][biodb::testThat]
biodb.INFO [2022-10-18 18:49:05.182][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2022-10-18 18:49:05.183][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:49:05.184][biodb::testThat]
biodb.DEBUG[2022-10-18 18:49:05.255][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2022-10-18 18:49:05.259][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:49:05.261][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:49:05.263][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2022-10-18 18:49:05.909][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2022-10-18 18:49:06.614][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:49:06.621][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2022-10-18 18:49:06.633][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2022-10-18 18:49:06.728][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2022-10-18 18:49:06.732][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:49:06.733][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:49:06.735][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2022-10-18 18:49:07.368][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2022-10-18 18:49:08.062][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:49:08.069][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2022-10-18 18:49:08.081][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2022-10-18 18:49:08.092][biodb::testThat]
biodb.INFO [2022-10-18 18:49:08.093][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2022-10-18 18:49:08.094][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:49:08.095][biodb::testThat]
biodb.INFO [2022-10-18 18:49:08.117][biodb::testThat]
biodb.INFO [2022-10-18 18:49:08.118][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2022-10-18 18:49:08.119][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:49:08.120][biodb::testThat]
biodb.DEBUG[2022-10-18 18:49:08.188][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2022-10-18 18:49:08.191][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:49:08.192][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:49:08.194][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2022-10-18 18:49:08.688][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2022-10-18 18:49:09.203][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:49:09.212][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2022-10-18 18:49:09.226][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2022-10-18 18:49:09.312][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2022-10-18 18:49:09.316][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:49:09.318][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2022-10-18 18:49:09.320][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:49:09.321][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2022-10-18 18:49:09.401][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2022-10-18 18:49:09.405][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:49:09.406][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:49:09.408][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2022-10-18 18:49:09.895][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2022-10-18 18:49:10.386][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:49:10.397][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2022-10-18 18:49:10.414][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2022-10-18 18:49:10.534][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2022-10-18 18:49:10.538][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:49:10.539][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:49:10.542][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2022-10-18 18:49:12.212][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2022-10-18 18:49:15.535][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:49:15.544][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2022-10-18 18:49:15.558][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2022-10-18 18:49:15.681][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2022-10-18 18:49:15.685][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:49:15.686][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:49:15.688][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2022-10-18 18:49:17.078][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2022-10-18 18:49:20.128][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:49:20.138][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2022-10-18 18:49:20.175][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2022-10-18 18:49:20.228][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 18:49:20.230][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-10-18 18:49:20.231][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-10-18 18:49:20.232][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 18:49:20.233][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.235][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.237][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 18:49:20.242][biodb::testContext]
biodb.INFO [2022-10-18 18:49:20.243][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:49:20.244][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2022-10-18 18:49:20.245][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 18:49:20.246][biodb::testContext]
biodb.INFO [2022-10-18 18:49:20.252][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:49:20.254][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 18:49:20.258][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:49:20.259][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 18:49:20.260][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 18:49:20.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.264][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 18:49:20.265][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 18:49:20.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.269][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 18:49:20.270][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 18:49:20.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.274][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 18:49:20.275][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 18:49:20.276][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 18:49:20.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.280][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 18:49:20.281][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 18:49:20.282][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 18:49:20.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.286][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 18:49:20.287][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 18:49:20.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.290][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 18:49:20.291][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 18:49:20.292][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 18:49:20.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.296][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 18:49:20.297][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 18:49:20.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.301][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 18:49:20.302][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 18:49:20.303][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 18:49:20.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.307][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:49:20.308][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 18:49:20.309][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 18:49:20.310][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 18:49:20.311][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 18:49:20.312][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 18:49:20.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.316][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 18:49:20.317][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 18:49:20.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.321][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 18:49:20.322][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 18:49:20.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.326][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 18:49:20.327][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 18:49:20.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.331][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 18:49:20.332][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 18:49:20.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.336][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 18:49:20.337][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 18:49:20.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.341][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 18:49:20.342][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 18:49:20.345][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 18:49:20.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.349][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 18:49:20.350][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 18:49:20.351][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 18:49:20.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.355][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 18:49:20.357][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.358][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 18:49:20.359][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.360][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:49:20.361][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.362][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.363][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.364][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.365][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:49:20.367][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:49:20.368][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.369][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 18:49:20.370][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:49:20.371][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.372][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.373][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:49:20.373][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:49:20.373][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:49:20.373][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:49:20.373][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:49:20.374][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:49:20.375][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:20.376][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:20.377][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:49:20.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:20.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:20.379][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.380][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.381][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:49:20.382][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:49:20.383][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.384][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.385][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 18:49:20.387][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.388][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:49:20.389][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.390][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:49:20.391][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.392][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.393][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.394][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.395][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:49:20.397][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:49:20.398][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.399][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 18:49:20.400][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:49:20.401][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.402][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.403][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:49:20.403][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:49:20.403][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 18:49:20.403][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 18:49:20.403][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 18:49:20.404][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:49:20.405][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:20.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:20.407][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:49:20.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:20.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:20.410][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.411][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.412][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:49:20.413][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:49:20.413][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.415][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.416][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 18:49:20.418][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.419][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 18:49:20.420][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.421][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:49:20.422][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.423][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.424][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.425][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.426][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:49:20.427][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:49:20.428][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.429][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 18:49:20.430][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:49:20.431][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.432][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.433][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.434][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:49:20.435][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:20.436][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:20.437][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:49:20.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:20.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:20.440][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.441][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.442][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:49:20.443][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:49:20.444][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.445][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.446][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 18:49:20.448][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.449][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 18:49:20.450][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.451][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:49:20.452][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.453][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.454][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.455][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.456][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 18:49:20.457][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:49:20.458][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.459][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 18:49:20.460][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:49:20.461][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.462][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.463][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.464][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:49:20.465][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:20.466][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:20.467][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:49:20.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:20.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:20.470][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.471][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.472][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:49:20.473][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:49:20.474][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.475][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.477][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:49:20.478][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.558][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[2022-10-18 18:49:20.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.571][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[2022-10-18 18:49:20.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.591][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 18:49:20.593][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 18:49:20.595][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 18:49:20.596][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 18:49:20.598][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 18:49:20.600][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 18:49:20.601][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 18:49:20.603][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 18:49:20.604][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 18:49:20.606][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 18:49:20.608][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 18:49:20.609][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 18:49:20.611][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 18:49:20.612][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 18:49:20.614][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 18:49:20.615][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:49:20.617][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 18:49:20.618][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 18:49:20.620][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 18:49:20.621][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 18:49:20.623][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 18:49:20.624][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 18:49:20.626][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 18:49:20.627][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 18:49:20.629][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 18:49:20.630][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 18:49:20.632][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 18:49:20.633][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 18:49:20.635][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 18:49:20.636][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 18:49:20.638][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 18:49:20.639][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 18:49:20.640][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 18:49:20.642][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 18:49:20.643][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 18:49:20.645][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 18:49:20.646][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 18:49:20.648][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 18:49:20.649][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 18:49:20.651][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 18:49:20.652][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 18:49:20.653][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 18:49:20.655][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 18:49:20.656][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 18:49:20.658][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 18:49:20.660][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 18:49:20.661][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 18:49:20.662][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 18:49:20.664][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 18:49:20.665][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 18:49:20.667][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 18:49:20.668][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 18:49:20.669][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 18:49:20.671][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 18:49:20.672][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 18:49:20.674][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 18:49:20.675][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 18:49:20.677][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 18:49:20.678][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 18:49:20.679][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 18:49:20.681][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 18:49:20.683][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 18:49:20.684][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 18:49:20.686][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 18:49:20.687][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 18:49:20.688][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 18:49:20.690][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 18:49:20.691][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 18:49:20.693][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 18:49:20.694][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 18:49:20.695][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 18:49:20.697][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 18:49:20.698][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 18:49:20.700][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 18:49:20.701][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 18:49:20.703][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 18:49:20.704][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 18:49:20.706][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 18:49:20.707][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 18:49:20.708][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 18:49:20.710][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 18:49:20.711][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 18:49:20.713][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 18:49:20.714][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 18:49:20.716][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 18:49:20.717][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 18:49:20.718][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.720][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 18:49:20.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:20.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:20.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:20.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:20.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:20.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:20.833][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-10-18 18:49:20.834][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 18:49:20.836][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.837][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.839][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.840][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 18:49:20.841][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.842][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.843][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.863][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.865][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 18:49:20.867][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 18:49:20.868][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.869][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-10-18 18:49:20.870][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 18:49:20.871][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-10-18 18:49:20.871][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-10-18 18:49:20.871][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-10-18 18:49:20.871][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-10-18 18:49:20.871][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-10-18 18:49:20.871][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-10-18 18:49:20.871][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-10-18 18:49:20.871][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-10-18 18:49:20.871][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-10-18 18:49:20.873][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 18:49:20.874][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 18:49:20.874][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 18:49:20.875][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 18:49:20.876][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:20.877][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:20.878][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 18:49:20.879][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 18:49:20.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 18:49:20.880][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 18:49:20.881][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 18:49:20.881][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-10-18 18:49:20.882][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 18:49:20.883][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 18:49:20.884][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 18:49:20.885][self$setPropertyValue]
biodb.DEBUG[2022-10-18 18:49:20.887][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-10-18 18:49:20.888][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 18:49:20.892][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 18:49:20.893][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-10-18 18:49:20.894][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 18:49:20.896][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-10-18 18:49:20.897][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 18:49:20.898][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 18:49:20.899][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-10-18 18:49:20.900][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-10-18 18:49:20.902][biodb::testThat]
biodb.INFO [2022-10-18 18:49:20.903][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2022-10-18 18:49:20.904][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 18:49:20.905][biodb::testThat]
biodb.DEBUG[2022-10-18 18:49:20.993][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2022-10-18 18:49:20.998][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 18:49:21.000][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2022-10-18 18:49:21.001][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 18:49:21.048][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2022-10-18 18:49:21.656][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2022-10-18 18:49:21.658][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-10-18 18:49:21.660][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2022-10-18 18:49:21.661][cch$loadFileContent] file.exist = [2]: "FALSE, TRUE".
biodb.TRACE[2022-10-18 18:49:21.663][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2022-10-18 18:49:21.664][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 18:49:21.665][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 18:49:21.666][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 18:49:21.667][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 18:49:21.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:49:21.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:21.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:21.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:21.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:21.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:21.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 18:49:21.683][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2022-10-18 18:49:21.687][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 18:49:21.688][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 18:49:21.689][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2022-10-18 18:49:22.625][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2022-10-18 18:49:23.567][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 18:49:23.589][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2022-10-18 18:49:23.617][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.TRACE[2022-10-18 18:49:23.640][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2022-10-18 18:49:23.649][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 18:49:23.679][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-10-18 18:49:23.681][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 18:49:23.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:49:23.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:23.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:23.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:23.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:23.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:23.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:49:23.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:23.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:23.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:23.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:23.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:23.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:23.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:23.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:23.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.815][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:49:23.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:49:23.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.823][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:49:23.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:49:23.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.830][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:23.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:23.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.837][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:23.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:23.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.850][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:23.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:23.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.858][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:23.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:23.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.873][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:49:23.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:23.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.878][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:49:23.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:23.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.887][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:23.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:23.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.892][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:23.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:23.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:23.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:23.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:23.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:23.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.916][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:49:23.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:23.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.921][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 18:49:23.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:23.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.926][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:23.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:23.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:23.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:23.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.935][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:49:23.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:23.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:23.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:23.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:23.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:23.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:23.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:23.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:23.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:23.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:23.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:23.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.971][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:23.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:23.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.976][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:23.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:23.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:23.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:23.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.985][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:23.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:23.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:23.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:23.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:23.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:23.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:23.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:23.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:49:24.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:49:24.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:24.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:24.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:24.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:24.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:24.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:49:24.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.055][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:49:24.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 18:49:24.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.061][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:49:24.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 18:49:24.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.066][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.071][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.080][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.094][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:49:24.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.099][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 18:49:24.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.109][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.114][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.128][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.136][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:49:24.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.141][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 18:49:24.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.150][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.154][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 18:49:24.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.163][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.168][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.177][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 18:49:24.254][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2022-10-18 18:49:24.257][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 18:49:24.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:49:24.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:24.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:24.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:24.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:24.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:24.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:49:24.273][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:49:24.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:49:24.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.277][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:49:24.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:49:24.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.282][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 18:49:24.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 18:49:24.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.286][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 18:49:24.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 18:49:24.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.291][private$selectFields] Fields none
biodb.TRACE[2022-10-18 18:49:24.292][private$selectFields]
biodb.TRACE[2022-10-18 18:49:24.293][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-10-18 18:49:24.293][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:49:24.295][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:49:24.296][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.297][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.298][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.299][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.300][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.302][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.303][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.304][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.305][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.306][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.307][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.308][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.309][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.310][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.311][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.312][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.313][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.315][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.316][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.317][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.318][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.319][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.320][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.321][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.322][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.323][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.324][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.325][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.326][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.327][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.328][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.329][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.330][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.332][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.333][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.334][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.335][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.336][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.337][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.338][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.339][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.341][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.342][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.343][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.344][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.345][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.347][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.348][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.349][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.350][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.351][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.352][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.354][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.355][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.356][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.357][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.358][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.359][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.361][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.362][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.363][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.364][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.365][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.367][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:49:24.368][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:49:24.369][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.370][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.371][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.373][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.374][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.375][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.376][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.377][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.379][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.380][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.381][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.382][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.384][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.385][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.386][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.387][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.388][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.389][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.390][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.391][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.393][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.394][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.395][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.396][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.397][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.398][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.399][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.400][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.402][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.403][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.404][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.405][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.406][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2022-10-18 18:49:24.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.435][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.439][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.443][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.448][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.453][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.457][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.475][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.484][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.489][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.502][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.506][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.511][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.521][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2022-10-18 18:49:24.523][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 18:49:24.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:24.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:24.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:24.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:24.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:24.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 18:49:24.537][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:49:24.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:49:24.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.541][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 18:49:24.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 18:49:24.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.545][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 18:49:24.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 18:49:24.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.570][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 18:49:24.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 18:49:24.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.575][private$selectFields] Fields none
biodb.TRACE[2022-10-18 18:49:24.576][private$selectFields]
biodb.TRACE[2022-10-18 18:49:24.578][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-10-18 18:49:24.579][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 18:49:24.580][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:49:24.581][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.582][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.583][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.584][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.585][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.587][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.588][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.589][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.590][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.591][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.592][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.593][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.594][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.595][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.596][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.597][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.598][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.599][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.600][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.601][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.602][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.603][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.604][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.605][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.606][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.607][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.608][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.609][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.610][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.611][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.612][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.613][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.614][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.615][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.616][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.617][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.618][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.620][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.621][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.622][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.623][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.624][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.625][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.626][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.627][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.628][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.629][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.630][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.631][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.632][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.633][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.634][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.635][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.636][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.637][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.638][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.639][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.640][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.641][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.642][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.643][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.644][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.645][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.646][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.647][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:49:24.649][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 18:49:24.650][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.651][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.652][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.653][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.654][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.655][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.656][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.657][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.658][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.659][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.660][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.661][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.663][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.664][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.665][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.666][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.667][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.668][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.669][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.670][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.671][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.673][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.674][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.675][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.676][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.677][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.678][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.679][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.680][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.681][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.682][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.683][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.684][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2022-10-18 18:49:24.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 18:49:24.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 18:49:24.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 18:49:24.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.713][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.717][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.721][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 18:49:24.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.726][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.730][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.734][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 18:49:24.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 18:49:24.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.752][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.761][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 18:49:24.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 18:49:24.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 18:49:24.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 18:49:24.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.778][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.782][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.787][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 18:49:24.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 18:49:24.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 18:49:24.795][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2022-10-18 18:49:24.796][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 18:49:24.797][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2022-10-18 18:49:24.801][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 18:49:24.803][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-10-18 18:49:24.804][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-10-18 18:49:24.805][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 18:49:24.806][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 18:49:24.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 18:49:24.808][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 18:49:24.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 18:49:24.810][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 18:49:24.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 169 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 169 ]
> 
> proc.time()
   user  system elapsed 
 21.509   1.712 135.109

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.1850.2412.449
LipidmapsStructureEntry0.3660.0000.367