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This page was generated on 2023-04-12 11:04:59 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 nebbiolo2


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 184/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.4.1  (landing page)
Pierrick Roger
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_16
git_last_commit: 75afc75
git_last_commit_date: 2022-12-01 07:31:40 -0400 (Thu, 01 Dec 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: biodbLipidmaps
Version: 1.4.1
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings biodbLipidmaps_1.4.1.tar.gz
StartedAt: 2023-04-10 19:18:48 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:22:11 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 203.3 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings biodbLipidmaps_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.4.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ...
  ‘biodbLipidmaps.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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 [2023-04-10 19:19:31.520][biodb::testContext]
biodb.INFO [2023-04-10 19:19:31.522][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:19:31.523][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-04-10 19:19:31.524][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:19:31.525][biodb::testContext]
biodb.INFO [2023-04-10 19:19:31.533][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:19:31.535][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:19:31.543][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:31.544][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:19:31.545][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:19:31.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.549][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:19:31.568][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:19:31.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.571][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[2023-04-10 19:19:31.572][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:19:31.574][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:19:31.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.577][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:19:31.578][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:19:31.579][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:19:31.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.587][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:19:31.589][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:19:31.590][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:19:31.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.594][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:19:31.595][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:19:31.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.598][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[2023-04-10 19:19:31.599][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:19:31.600][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:19:31.601][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:19:31.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.605][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:19:31.606][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:19:31.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.609][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[2023-04-10 19:19:31.610][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:19:31.611][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:19:31.612][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:19:31.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.615][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:19:31.616][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:19:31.617][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:19:31.618][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:19:31.620][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:19:31.621][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:19:31.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.624][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:19:31.626][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:19:31.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.629][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:19:31.630][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:19:31.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.634][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:19:31.635][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:19:31.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.639][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:19:31.640][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:19:31.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.643][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[2023-04-10 19:19:31.644][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:19:31.645][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:19:31.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.649][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:19:31.650][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:19:31.655][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:19:31.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.659][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:19:31.660][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:19:31.661][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:19:31.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.669][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:19:31.706][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.724][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-10 19:19:31.725][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.726][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:31.728][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.729][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.730][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.730][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.732][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:19:31.733][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:31.734][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.735][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:19:31.736][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:31.737][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.738][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.739][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:31.739][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:19:31.739][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:19:31.739][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:19:31.739][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:19:31.740][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:31.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:31.742][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:31.743][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:31.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:31.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:31.760][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.761][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.762][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:31.763][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:31.764][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.765][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.766][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:19:31.768][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.769][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:19:31.769][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.770][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:31.771][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.772][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.773][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.774][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.775][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:19:31.776][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:31.777][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.778][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:19:31.779][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:31.780][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.781][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.782][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:31.782][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:19:31.782][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:19:31.782][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:19:31.782][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:19:31.783][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:31.784][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:31.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:31.786][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:31.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:31.788][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:31.789][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.790][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.791][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:31.792][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:31.793][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.794][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.795][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:19:31.797][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.798][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-10 19:19:31.799][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.800][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:31.801][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.802][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.803][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.804][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.805][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:19:31.806][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:31.807][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.808][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:19:31.809][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:31.810][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.811][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.813][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.814][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:31.815][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:31.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:31.817][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:31.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:31.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:31.820][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.821][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.822][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:31.823][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:31.824][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.825][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.826][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:19:31.828][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.829][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:19:31.830][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.831][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:31.832][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.833][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.833][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.834][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.835][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:19:31.836][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:31.837][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.838][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:19:31.839][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:31.840][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.841][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:31.842][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.843][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:31.844][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:31.845][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:31.846][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:31.847][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:31.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:31.849][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:31.850][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.851][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:31.852][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:31.853][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:31.854][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:31.859][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:31.860][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.874][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[2023-04-10 19:19:31.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.878][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[2023-04-10 19:19:31.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.910][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[2023-04-10 19:19:31.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:31.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:31.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:31.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:31.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:31.931][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:19:31.936][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:19:31.938][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:19:31.939][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:19:31.940][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:19:31.941][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:19:31.943][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:19:31.944][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:19:31.945][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:19:31.946][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:19:31.948][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:19:31.949][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:19:31.950][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:19:31.951][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:19:31.953][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:19:31.954][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:19:31.955][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:19:31.956][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:19:31.957][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:19:31.959][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:19:31.960][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:19:31.961][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:19:31.962][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:19:31.964][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:19:31.965][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:19:31.966][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:19:31.967][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:19:31.969][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:19:31.970][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:19:31.971][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:19:31.973][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:19:31.974][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:19:31.975][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:19:31.976][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:19:31.978][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:19:31.979][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:19:31.980][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:19:31.981][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:19:31.983][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:19:31.984][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:19:31.985][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:19:31.986][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:19:31.988][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:19:31.989][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:19:31.990][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:19:31.991][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:19:31.993][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:19:31.994][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:19:31.995][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:19:31.996][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:19:31.998][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:19:31.999][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:19:32.000][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:19:32.002][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:19:32.003][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:19:32.004][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:19:32.011][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:19:32.012][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:19:32.014][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:19:32.015][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:19:32.016][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:19:32.017][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:19:32.018][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:19:32.020][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:19:32.021][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:19:32.022][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:19:32.023][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:19:32.024][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:19:32.026][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:19:32.027][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:19:32.028][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:19:32.029][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:19:32.031][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:19:32.032][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:19:32.033][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:19:32.034][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:19:32.035][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:19:32.037][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:19:32.038][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:19:32.039][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:19:32.040][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:19:32.042][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:19:32.043][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:19:32.048][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:19:32.050][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:19:32.053][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:19:32.054][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.055][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.066][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[2023-04-10 19:19:32.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.142][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[2023-04-10 19:19:32.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:19:32.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:32.161][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-04-10 19:19:32.169][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:19:32.171][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:32.172][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:19:32.173][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:32.174][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:19:32.175][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:32.176][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:19:32.177][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:32.178][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:19:32.179][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:19:32.180][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:19:32.181][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:32.182][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-04-10 19:19:32.183][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:19:32.184][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-04-10 19:19:32.184][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-04-10 19:19:32.184][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-04-10 19:19:32.184][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-04-10 19:19:32.184][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-04-10 19:19:32.184][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-04-10 19:19:32.184][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-04-10 19:19:32.184][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-04-10 19:19:32.184][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-04-10 19:19:32.185][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:19:32.185][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:19:32.185][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:19:32.186][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:19:32.187][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:32.188][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:32.189][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:19:32.190][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:19:32.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:19:32.192][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:19:32.192][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-10 19:19:32.192][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-04-10 19:19:32.193][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:19:32.194][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:19:32.195][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:19:32.196][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:19:32.202][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-04-10 19:19:32.203][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:19:32.228][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:19:32.229][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-04-10 19:19:32.234][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:19:32.238][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-04-10 19:19:32.243][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-10 19:19:32.244][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-10 19:19:32.245][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-04-10 19:19:32.246][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-04-10 19:19:32.254][biodb::testThat]
biodb.INFO [2023-04-10 19:19:32.256][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-04-10 19:19:32.256][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:32.257][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:32.261][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-04-10 19:19:32.263][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:32.274][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-10 19:19:32.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:32.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.300][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.TRACE[2023-04-10 19:19:32.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.335][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:32.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:32.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.339][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.343][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.368][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.372][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.376][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.380][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:19:32.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.384][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:19:32.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.388][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.392][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.403][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:19:32.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.407][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:19:32.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.411][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.418][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:19:32.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.436][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.440][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.471][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.504][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.508][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.514][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:32.539][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-04-10 19:19:32.541][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:32.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:32.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.544][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:32.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:32.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.548][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:32.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:32.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.551][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:32.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:32.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.584][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.614][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.617][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.620][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.641][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.642][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.642][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.643][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.654][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.657][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.661][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.664][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.665][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.666][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.667][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.677][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.681][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.684][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.688][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.689][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.690][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.690][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.691][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.705][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.709][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.712][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.715][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.716][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.717][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.718][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.719][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.739][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.740][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.741][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.741][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.752][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.755][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.759][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.762][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.763][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.764][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.765][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.765][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.775][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.776][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.777][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.778][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.782][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.783][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.784][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.785][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.790][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.791][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.792][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.792][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.797][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.798][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.799][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.800][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.804][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.805][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.806][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.807][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.811][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.812][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.813][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.814][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:32.819][biodb::testThat]
biodb.INFO [2023-04-10 19:19:32.820][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-10 19:19:32.821][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:32.822][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:32.834][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-04-10 19:19:32.841][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:19:32.844][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-04-10 19:19:32.845][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:32.847][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-04-10 19:19:32.848][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:19:32.868][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:19:32.869][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-10 19:19:32.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:32.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:32.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:32.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:32.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:32.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:32.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:19:32.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:19:32.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.903][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:32.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:19:32.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.907][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:19:32.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.910][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.914][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:19:32.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.917][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.921][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:19:32.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.925][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:19:32.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.928][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:19:32.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:32.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.932][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.935][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:19:32.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:19:32.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.946][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:19:32.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.950][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:19:32.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.960][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:19:32.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:32.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:32.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.982][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.985][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.992][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:19:32.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:32.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:32.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:32.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:32.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:19:33.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:19:33.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.017][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-04-10 19:19:33.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-10 19:19:33.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-10 19:19:33.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-10 19:19:33.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-10 19:19:33.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-10 19:19:33.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-10 19:19:33.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:33.033][biodb::testThat]
biodb.INFO [2023-04-10 19:19:33.034][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-10 19:19:33.035][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:33.036][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:33.038][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.039][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.040][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.041][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.042][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-04-10 19:19:33.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:33.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:33.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:33.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:33.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:33.078][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-04-10 19:19:33.216][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[2023-04-10 19:19:33.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:33.236][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:33.237][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-04-10 19:19:34.638][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-04-10 19:19:35.608][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:35.611][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-04-10 19:19:35.628][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-04-10 19:19:35.631][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-04-10 19:19:35.646][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:35.647][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:35.648][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.649][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:35.652][biodb::testThat]
biodb.INFO [2023-04-10 19:19:35.653][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-04-10 19:19:35.654][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:35.655][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:35.693][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:35.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:35.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.700][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:35.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:35.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:35.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:35.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:35.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:35.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:35.907][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-04-10 19:19:35.918][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:19:35.943][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-04-10 19:19:35.946][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:35.948][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-04-10 19:19:35.982][biodb::testThat]
biodb.INFO [2023-04-10 19:19:35.983][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-04-10 19:19:35.985][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:35.986][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:36.022][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:36.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:36.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.029][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:36.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:36.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.035][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:36.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:36.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.094][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:36.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:36.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.159][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:36.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:36.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.164][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:19:36.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:19:36.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:36.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:19:36.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:36.172][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:36.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:19:36.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:36.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:36.180][biodb::testThat]
biodb.INFO [2023-04-10 19:19:36.181][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-10 19:19:36.182][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:36.183][biodb::testThat]
biodb.INFO [2023-04-10 19:19:36.189][biodb::testThat]
biodb.INFO [2023-04-10 19:19:36.190][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-10 19:19:36.191][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:36.192][biodb::testThat]
biodb.INFO [2023-04-10 19:19:36.198][biodb::testThat]
biodb.INFO [2023-04-10 19:19:36.199][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-10 19:19:36.200][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:36.201][biodb::testThat]
biodb.DEBUG[2023-04-10 19:19:36.206][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-04-10 19:19:37.306][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-04-10 19:19:37.749][biodb::testThat]
biodb.INFO [2023-04-10 19:19:37.751][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-10 19:19:37.753][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:37.755][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:37.761][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:37.763][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:37.764][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.766][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.768][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:37.769][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:37.771][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.772][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:37.775][biodb::testThat]
biodb.INFO [2023-04-10 19:19:37.777][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-04-10 19:19:37.778][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:37.780][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:37.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:37.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:37.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:37.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:37.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:37.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:19:37.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:19:37.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:37.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:38.064][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-04-10 19:19:38.068][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:19:38.069][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-04-10 19:19:38.071][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:38.072][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-04-10 19:19:38.203][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-04-10 19:19:38.206][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:19:38.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-04-10 19:19:38.209][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:19:38.211][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-04-10 19:19:38.232][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:38.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:38.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:38.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:38.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:38.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:38.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:38.295][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-04-10 19:19:38.311][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:38.312][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:38.327][private$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[2023-04-10 19:19:42.282][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[2023-04-10 19:19:53.717][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2023-04-10 19:19:53.719][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2023-04-10 19:19:53.721][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2023-04-10 19:19:53.735][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2023-04-10 19:19:54.671][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-04-10 19:19:54.675][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:54.677][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:54.679][private$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[2023-04-10 19:19:55.336][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[2023-04-10 19:19:56.000][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:56.003][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2023-04-10 19:19:56.011][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2023-04-10 19:19:56.075][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[2023-04-10 19:19:56.080][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:56.082][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:56.085][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2023-04-10 19:19:56.745][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2023-04-10 19:19:57.399][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:19:57.403][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2023-04-10 19:19:57.409][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2023-04-10 19:19:57.440][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-10 19:19:57.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-10 19:19:57.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:57.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:19:57.458][biodb::testThat]
biodb.INFO [2023-04-10 19:19:57.459][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-04-10 19:19:57.461][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:19:57.462][biodb::testThat]
biodb.TRACE[2023-04-10 19:19:57.468][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:19:57.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:19:57.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:57.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:57.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:57.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:19:57.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:57.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:57.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:57.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:57.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:57.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:57.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:57.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:57.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:57.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:57.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:57.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:57.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:57.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:19:57.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:57.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:19:57.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:19:57.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:19:57.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:19:57.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:19:57.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:19:57.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:19:57.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:19:57.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:19:57.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:19:57.654][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-04-10 19:19:57.658][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:19:57.659][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:19:57.661][private$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[2023-04-10 19:20:01.678][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[2023-04-10 19:20:13.107][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:13.110][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-04-10 19:20:13.125][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-04-10 19:20:14.088][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-04-10 19:20:14.137][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-10 19:20:14.139][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-04-10 19:20:14.141][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-04-10 19:20:14.142][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:20:14.143][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:20:14.144][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-10 19:20:14.145][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:20:14.146][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:20:14.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:14.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:14.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:14.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:14.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:14.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:14.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:14.175][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-04-10 19:20:14.178][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:14.179][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:14.181][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-04-10 19:20:14.842][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-04-10 19:20:15.471][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:15.475][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-04-10 19:20:15.482][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-04-10 19:20:15.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:15.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:15.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:15.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:15.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:15.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:15.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:15.503][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-04-10 19:20:15.508][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:15.509][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:15.511][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-04-10 19:20:16.141][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-04-10 19:20:16.801][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:16.804][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-04-10 19:20:16.809][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-04-10 19:20:16.813][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2023-04-10 19:20:16.815][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:20:16.817][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-04-10 19:20:16.818][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-10 19:20:16.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:16.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:16.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:16.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:16.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:16.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:16.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:16.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:16.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:16.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:16.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.887][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:20:16.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:20:16.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.892][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:16.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:16.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.897][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:20:16.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:20:16.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.902][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:20:16.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:20:16.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.908][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:20:16.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:20:16.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.913][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:20:16.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:20:16.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.921][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:20:16.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:16.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.928][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:20:16.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:16.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.932][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:20:16.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:20:16.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.935][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:20:16.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:20:16.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:16.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:16.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:16.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:16.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.946][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:20:16.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:16.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.949][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:20:16.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:16.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:16.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:16.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:16.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:16.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.960][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:20:16.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:16.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.963][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:16.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:16.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.967][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:16.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:16.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:16.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:16.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.975][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:16.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:16.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:16.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:16.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:16.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:16.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:16.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:16.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:16.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:16.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:16.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:16.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:16.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:16.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:16.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:16.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:16.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:17.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:17.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:17.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:17.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:17.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:20:17.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:20:17.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.025][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:20:17.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:20:17.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.029][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:17.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:20:17.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.032][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:20:17.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:20:17.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.036][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:20:17.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:20:17.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.039][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:20:17.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:20:17.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.043][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:20:17.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:20:17.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.047][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:20:17.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:17.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.050][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:20:17.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:17.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.054][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:20:17.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:20:17.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.057][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:20:17.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:20:17.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.061][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:17.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:17.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:17.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:17.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.068][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:20:17.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:17.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.071][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:20:17.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:17.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.075][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:17.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:17.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:20:17.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:17.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.081][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:20:17.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:20:17.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.085][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.088][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:17.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:17.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.095][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:17.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:17.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:17.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:17.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:17.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:17.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:17.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:17.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:17.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:17.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:17.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:17.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:17.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:17.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:17.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:17.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:17.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:17.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:17.128][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-04-10 19:20:17.137][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:20:17.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:17.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:17.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:17.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:17.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:17.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:17.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:17.148][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.163][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.167][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:17.168][private$selectFields]
biodb.TRACE[2023-04-10 19:20:17.168][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:17.169][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:17.170][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:17.171][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.172][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.173][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.174][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.174][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.175][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.176][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.177][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.178][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:17.179][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:17.180][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.180][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.181][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.182][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.183][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:20:17.184][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.187][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.191][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.201][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-04-10 19:20:17.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:17.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:17.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:17.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:17.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:17.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:17.211][FUN] Functions in observer BiodbConfig: [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[2023-04-10 19:20:17.212][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.216][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.219][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:17.220][private$selectFields]
biodb.TRACE[2023-04-10 19:20:17.221][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:17.221][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:17.222][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:17.223][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.224][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.225][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.225][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.226][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.227][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.228][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.229][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.230][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:17.230][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:17.231][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.232][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.233][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.234][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.234][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:20:17.235][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.239][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.242][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.246][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-04-10 19:20:17.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:17.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:17.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:17.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:17.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:17.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:17.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:17.256][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.259][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.263][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:17.264][private$selectFields]
biodb.TRACE[2023-04-10 19:20:17.264][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:17.265][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:17.266][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:17.267][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.268][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.269][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.269][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.270][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.271][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.272][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.273][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.274][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:17.274][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:17.275][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.276][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.277][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.278][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.279][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:20:17.280][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.283][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.297][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:17.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.301][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-04-10 19:20:17.301][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:20:17.302][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-10 19:20:17.310][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:17.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:17.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:20:17.315][biodb::testThat]
biodb.INFO [2023-04-10 19:20:17.316][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-04-10 19:20:17.317][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:17.317][biodb::testThat]
biodb.TRACE[2023-04-10 19:20:17.320][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:20:17.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:20:17.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:17.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:17.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:17.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:17.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:17.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:17.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:17.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:17.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:17.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:17.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:17.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:17.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:17.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:17.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:17.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:17.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:17.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:17.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:17.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:17.497][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2023-04-10 19:20:17.515][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:17.516][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:17.518][private$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[2023-04-10 19:20:21.324][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[2023-04-10 19:20:32.508][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:20:32.511][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2023-04-10 19:20:32.525][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2023-04-10 19:20:33.522][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:20:33.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:33.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:33.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:33.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:33.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:33.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:33.552][FUN] Functions in observer BiodbConfig: [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[2023-04-10 19:20:33.563][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.567][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.588][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:33.589][private$selectFields]
biodb.TRACE[2023-04-10 19:20:33.590][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:33.591][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:33.592][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:33.593][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.594][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.595][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.596][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.597][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.598][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.598][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.599][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.600][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:33.636][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:33.637][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.638][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.639][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.640][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.641][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:20:33.642][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.645][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.649][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.659][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-04-10 19:20:33.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:33.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:33.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:33.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:33.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:33.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:33.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:33.674][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.678][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.682][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:33.683][private$selectFields]
biodb.TRACE[2023-04-10 19:20:33.684][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:33.685][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:33.686][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:33.687][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.688][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.689][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.690][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.691][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.692][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.693][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.694][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.694][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:33.696][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:33.696][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.697][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.698][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.699][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.700][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:20:33.701][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.705][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.709][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.713][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-04-10 19:20:33.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:33.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:33.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:33.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:33.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:33.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:33.724][FUN] Functions in observer BiodbConfig: [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[2023-04-10 19:20:33.725][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.729][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.733][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:33.734][private$selectFields]
biodb.TRACE[2023-04-10 19:20:33.735][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:33.736][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:33.737][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:33.738][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.739][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.740][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.741][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.742][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.743][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.744][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.745][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.746][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:33.747][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:33.748][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.749][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.750][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.751][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.752][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:20:33.753][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.757][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.761][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:33.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.765][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-04-10 19:20:33.766][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:20:33.767][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-10 19:20:33.776][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:33.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:33.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:20:33.782][biodb::testThat]
biodb.INFO [2023-04-10 19:20:33.783][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-04-10 19:20:33.784][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:33.784][biodb::testThat]
biodb.TRACE[2023-04-10 19:20:33.788][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-10 19:20:33.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-10 19:20:33.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:33.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-10 19:20:33.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:33.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:33.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:33.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:33.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:33.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:33.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:33.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:33.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:20:33.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:33.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:33.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:33.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:33.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:33.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:33.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:33.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:33.842][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[2023-04-10 19:20:33.929][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[2023-04-10 19:20:33.932][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:20:33.934][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-04-10 19:20:33.935][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:20:33.986][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-04-10 19:20:34.742][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:20:34.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:34.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:34.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:34.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:34.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:34.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:34.753][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.TRACE[2023-04-10 19:20:34.754][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.758][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.781][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:34.782][private$selectFields]
biodb.TRACE[2023-04-10 19:20:34.783][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:34.784][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:34.785][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:34.785][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.786][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.787][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.788][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.789][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.790][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.791][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.792][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.793][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:34.794][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:34.794][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.795][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.796][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.797][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.798][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:20:34.799][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.802][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.806][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.810][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-04-10 19:20:34.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:34.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:34.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:34.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:34.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:34.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:34.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:34.821][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.824][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.828][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:34.829][private$selectFields]
biodb.TRACE[2023-04-10 19:20:34.830][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:34.830][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:34.831][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:34.832][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.833][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.834][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.835][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.836][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.837][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.837][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.838][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.839][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:34.840][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:34.841][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.842][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.843][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.843][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.844][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:20:34.845][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.849][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.852][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.856][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-04-10 19:20:34.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:34.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:34.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:34.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:34.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:34.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:34.866][FUN] Functions in observer BiodbConfig: [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[2023-04-10 19:20:34.867][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.870][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.874][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:34.874][private$selectFields]
biodb.TRACE[2023-04-10 19:20:34.875][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-10 19:20:34.876][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:20:34.877][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:34.878][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.879][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.880][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.881][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.881][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.882][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.883][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.884][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.885][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:34.886][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:20:34.887][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.888][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.888][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.889][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.890][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-10 19:20:34.891][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.894][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.898][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:34.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:34.902][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-04-10 19:20:34.903][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:20:34.904][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-10 19:20:34.932][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:34.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-10 19:20:34.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:34.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-10 19:20:34.937][biodb::testThat]
biodb.INFO [2023-04-10 19:20:34.938][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-04-10 19:20:34.939][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:34.940][biodb::testThat]
biodb.DEBUG[2023-04-10 19:20:34.942][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-04-10 19:20:34.943][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-10 19:20:34.944][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-04-10 19:20:34.946][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-10 19:20:34.947][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:20:34.948][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:20:34.949][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-10 19:20:34.949][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:20:34.950][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:20:34.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:34.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:34.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:34.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:34.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:34.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:34.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:34.974][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-04-10 19:20:34.977][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:34.978][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:34.979][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-10 19:20:35.573][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:35.575][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:35.576][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[2023-04-10 19:20:35.578][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-10 19:20:36.590][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-10 19:20:36.592][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:36.595][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:36.596][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-10 19:20:37.197][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:37.199][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:37.201][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[2023-04-10 19:20:37.202][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-10 19:20:38.104][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-10 19:20:38.106][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:38.108][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:38.111][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-10 19:20:38.722][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:38.724][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:38.725][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[2023-04-10 19:20:38.727][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-10 19:20:39.629][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-10 19:20:39.630][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:39.632][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:39.633][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-10 19:20:40.236][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:40.238][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:40.240][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[2023-04-10 19:20:40.242][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-10 19:20:41.091][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-10 19:20:41.094][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:41.096][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:41.098][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-10 19:20:41.715][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:41.717][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:41.719][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[2023-04-10 19:20:41.721][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-10 19:20:42.606][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-10 19:20:42.608][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:42.610][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:42.612][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-10 19:20:43.226][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:43.228][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:43.230][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[2023-04-10 19:20:43.232][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-10 19:20:44.117][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-10 19:20:44.119][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:44.121][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:44.124][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-10 19:20:44.743][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:44.745][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:44.747][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[2023-04-10 19:20:44.749][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-10 19:20:45.656][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-10 19:20:45.659][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:45.660][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:45.663][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-10 19:20:46.292][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:46.294][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:46.297][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[2023-04-10 19:20:46.299][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-10 19:20:47.185][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-10 19:20:47.188][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:47.190][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:47.193][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-10 19:20:47.815][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:47.817][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:47.819][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[2023-04-10 19:20:47.821][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-10 19:20:48.708][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-10 19:20:48.710][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:48.712][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:48.715][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-10 19:20:49.315][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:49.317][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:49.319][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[2023-04-10 19:20:49.344][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-10 19:20:50.208][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2023-04-10 19:20:50.213][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-04-10 19:20:50.216][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:20:50.217][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-04-10 19:20:50.218][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-10 19:20:50.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:50.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:50.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:50.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:50.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:50.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:50.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:20:50.230][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:50.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:50.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:50.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:50.233][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:50.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:20:50.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:50.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:50.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:50.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:50.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:50.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:50.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:50.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:50.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:50.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:50.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:50.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:50.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:50.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:50.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:50.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:50.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:50.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:50.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:50.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:50.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:50.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:20:50.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:20:50.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:20:50.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:20:50.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:20:50.257][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-04-10 19:20:50.258][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-04-10 19:20:50.264][biodb::testThat]
biodb.INFO [2023-04-10 19:20:50.265][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-04-10 19:20:50.265][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:20:50.266][biodb::testThat]
biodb.DEBUG[2023-04-10 19:20:50.273][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-04-10 19:20:50.273][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-04-10 19:20:50.274][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-10 19:20:50.276][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-04-10 19:20:50.277][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-04-10 19:20:50.278][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-10 19:20:50.279][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:20:50.280][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-10 19:20:50.280][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:20:50.281][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:20:50.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:20:50.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:20:50.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:20:50.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:20:50.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:20:50.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:20:50.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:20:50.294][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-04-10 19:20:50.297][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:50.297][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:50.298][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-10 19:20:50.897][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:50.898][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:50.900][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-10 19:20:50.902][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-10 19:20:51.784][private$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[2023-04-10 19:20:51.786][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:51.788][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:51.790][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-10 19:20:52.419][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:52.421][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:52.423][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-10 19:20:52.425][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-10 19:20:53.313][private$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[2023-04-10 19:20:53.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:53.318][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:53.321][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-10 19:20:53.936][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:53.938][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:53.940][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-10 19:20:53.941][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-10 19:20:54.828][private$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[2023-04-10 19:20:54.830][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:54.831][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:54.833][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-10 19:20:55.435][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:55.438][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:55.440][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-10 19:20:55.441][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-10 19:20:56.342][private$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[2023-04-10 19:20:56.343][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:56.345][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:56.347][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-10 19:20:56.952][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:56.953][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:56.955][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-10 19:20:56.956][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-10 19:20:57.860][private$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[2023-04-10 19:20:57.862][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:57.865][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:57.868][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-10 19:20:58.472][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:20:58.474][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:20:58.477][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-10 19:20:58.489][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-10 19:20:59.397][private$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[2023-04-10 19:20:59.398][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:20:59.400][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:20:59.402][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-10 19:21:00.024][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:21:00.026][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:21:00.027][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-10 19:21:00.029][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-10 19:21:00.924][private$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[2023-04-10 19:21:00.927][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:21:00.929][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:21:00.931][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-10 19:21:01.546][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:21:01.548][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:21:01.550][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-10 19:21:01.552][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-10 19:21:02.453][private$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[2023-04-10 19:21:02.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:21:02.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:21:02.459][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-10 19:21:03.067][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:21:03.069][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:21:03.072][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-10 19:21:03.074][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-10 19:21:03.924][private$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[2023-04-10 19:21:03.926][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:21:03.928][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:21:03.930][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-10 19:21:04.540][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-10 19:21:04.542][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-10 19:21:04.544][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-10 19:21:04.545][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-10 19:21:05.390][private$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[2023-04-10 19:21:05.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:21:05.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:05.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:05.402][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:05.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:05.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:05.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:05.407][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-04-10 19:21:05.411][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:21:05.412][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:21:05.413][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-04-10 19:21:06.046][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-04-10 19:21:06.675][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:21:06.680][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-04-10 19:21:06.683][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-04-10 19:21:06.686][private$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[2023-04-10 19:21:06.688][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:21:06.689][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-04-10 19:21:06.690][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-10 19:21:06.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:21:06.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:06.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:06.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:06.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:06.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:06.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:21:06.705][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:06.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:06.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.709][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:06.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:06.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:21:06.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:21:06.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:06.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:06.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:06.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:06.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:06.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:21:06.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:06.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:06.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:06.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:06.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.751][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:21:06.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:21:06.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.755][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:21:06.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:21:06.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.760][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:21:06.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:21:06.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.765][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:21:06.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:21:06.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.769][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:06.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:06.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.774][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:06.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:06.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.817][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:06.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:06.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.823][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:06.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:06.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.829][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:21:06.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:06.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.835][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:21:06.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:06.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.840][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:06.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:06.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.846][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:06.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:06.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:06.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:06.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:06.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:06.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.863][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:21:06.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:06.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.869][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:21:06.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:06.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:06.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:06.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:06.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:06.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.887][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:21:06.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:06.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:06.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:06.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:06.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:06.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:06.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:06.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.914][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:06.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:06.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:06.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:06.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.921][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:06.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:06.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.925][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:06.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:06.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.933][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:06.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:06.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:06.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:06.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:06.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:06.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:21:06.978][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-04-10 19:21:06.979][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-04-10 19:21:06.980][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-04-10 19:21:06.992][biodb::testThat]
biodb.INFO [2023-04-10 19:21:07.004][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-04-10 19:21:07.005][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:21:07.006][biodb::testThat]
biodb.INFO [2023-04-10 19:21:07.025][biodb::testThat]
biodb.INFO [2023-04-10 19:21:07.026][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-04-10 19:21:07.027][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:21:07.028][biodb::testThat]
biodb.INFO [2023-04-10 19:21:07.035][biodb::testThat]
biodb.INFO [2023-04-10 19:21:07.036][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-04-10 19:21:07.037][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:21:07.038][biodb::testThat]
biodb.DEBUG[2023-04-10 19:21:07.116][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-04-10 19:21:07.119][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:21:07.120][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:21:07.122][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-04-10 19:21:11.107][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-04-10 19:21:22.149][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:21:22.152][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-04-10 19:21:22.167][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-04-10 19:21:22.966][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:22.967][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:22.968][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:22.969][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:22.970][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:22.971][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:22.972][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:22.973][ef$get] fields variable is a list.
biodb.INFO [2023-04-10 19:21:22.974][biodb::testThat]
biodb.INFO [2023-04-10 19:21:22.975][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-04-10 19:21:22.976][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:21:22.977][biodb::testThat]
biodb.ERROR[2023-04-10 19:21:22.990][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-04-10 19:21:23.006][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-04-10 19:21:23.016][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:21:23.017][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-04-10 19:21:23.018][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-04-10 19:21:23.019][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:21:23.020][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.022][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.023][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.024][FUN] Functions in observer BiodbConfig: [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 [2023-04-10 19:21:23.035][biodb::testContext]
biodb.INFO [2023-04-10 19:21:23.036][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:21:23.037][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-04-10 19:21:23.038][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:21:23.038][biodb::testContext]
biodb.INFO [2023-04-10 19:21:23.041][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:21:23.042][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:21:23.046][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:21:23.047][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:21:23.048][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:21:23.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.052][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:21:23.053][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:21:23.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.056][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:21:23.057][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:21:23.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.061][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:21:23.061][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:21:23.062][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:21:23.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.066][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:21:23.067][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:21:23.068][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:21:23.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.071][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:21:23.072][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:21:23.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.075][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:21:23.076][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:21:23.077][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:21:23.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.081][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:21:23.082][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:21:23.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.085][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:21:23.086][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:21:23.087][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:21:23.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.091][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:21:23.092][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:21:23.093][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:21:23.094][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:21:23.095][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:21:23.096][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:21:23.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.099][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:21:23.100][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:21:23.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.120][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:21:23.121][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:21:23.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.125][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:21:23.126][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:21:23.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.129][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:21:23.130][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:21:23.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.134][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:21:23.135][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:21:23.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.138][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:21:23.139][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:21:23.144][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:21:23.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.147][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[2023-04-10 19:21:23.148][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:21:23.148][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:21:23.149][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:21:23.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.153][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:21:23.155][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.156][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-10 19:21:23.157][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.157][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:21:23.158][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.159][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.160][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.161][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.162][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:21:23.163][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:21:23.164][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.165][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:21:23.166][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:21:23.167][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.168][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.168][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:21:23.168][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:21:23.168][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:21:23.168][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:21:23.168][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:21:23.169][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:21:23.170][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:23.171][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:23.172][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:21:23.173][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:23.174][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:23.175][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.176][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.177][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:21:23.177][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:21:23.178][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.179][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.180][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:21:23.182][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.183][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:21:23.184][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.185][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:21:23.186][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.187][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.188][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.189][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.190][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:21:23.190][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:21:23.191][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.192][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:21:23.193][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:21:23.194][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.195][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.196][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:21:23.196][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:21:23.196][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:21:23.196][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:21:23.196][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:21:23.197][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:21:23.198][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:23.199][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:23.200][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:21:23.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:23.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:23.203][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.204][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.205][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:21:23.205][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:21:23.206][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.207][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.208][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:21:23.210][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.211][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-10 19:21:23.212][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.213][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:21:23.214][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.216][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.218][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:21:23.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:21:23.220][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.221][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:21:23.222][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:21:23.223][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.224][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.225][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.226][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:21:23.226][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:23.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:23.228][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:21:23.229][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:23.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:23.231][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.232][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.233][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:21:23.234][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:21:23.234][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.235][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.237][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:21:23.238][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.239][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:21:23.240][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.241][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:21:23.242][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.243][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.244][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.245][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.246][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:21:23.247][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:21:23.248][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.249][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:21:23.250][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:21:23.256][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.258][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.259][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.261][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:21:23.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:23.263][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:23.264][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:21:23.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:23.295][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:23.297][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.298][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.299][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:21:23.300][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:21:23.301][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.302][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.303][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:21:23.304][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.365][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[2023-04-10 19:21:23.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.383][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[2023-04-10 19:21:23.384][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:21:23.385][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:21:23.387][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:21:23.388][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:21:23.390][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:21:23.391][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:21:23.393][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:21:23.394][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:21:23.396][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:21:23.397][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:21:23.399][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:21:23.400][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:21:23.402][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:21:23.403][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:21:23.405][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:21:23.407][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:21:23.408][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:21:23.410][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:21:23.412][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:21:23.413][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:21:23.415][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:21:23.416][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:21:23.418][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:21:23.419][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:21:23.421][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:21:23.423][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:21:23.425][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:21:23.426][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:21:23.428][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:21:23.429][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:21:23.431][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:21:23.433][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:21:23.434][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:21:23.436][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:21:23.437][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:21:23.439][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:21:23.440][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:21:23.441][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:21:23.443][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:21:23.457][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:21:23.459][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:21:23.460][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:21:23.462][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:21:23.463][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:21:23.464][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:21:23.466][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:21:23.467][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:21:23.468][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:21:23.470][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:21:23.471][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:21:23.472][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:21:23.474][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:21:23.475][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:21:23.476][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:21:23.477][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:21:23.479][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:21:23.480][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:21:23.481][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:21:23.483][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:21:23.484][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:21:23.486][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:21:23.487][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:21:23.488][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:21:23.490][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:21:23.491][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:21:23.492][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:21:23.493][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:21:23.495][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:21:23.496][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:21:23.497][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:21:23.499][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:21:23.500][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:21:23.502][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:21:23.503][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:21:23.504][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:21:23.505][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:21:23.507][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:21:23.508][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:21:23.509][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:21:23.511][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:21:23.512][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:21:23.513][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:21:23.514][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:21:23.516][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:21:23.517][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:21:23.518][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:21:23.519][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.521][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.556][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.DEBUG[2023-04-10 19:21:23.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.562][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[2023-04-10 19:21:23.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.567][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[2023-04-10 19:21:23.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.585][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[2023-04-10 19:21:23.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:23.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:23.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:23.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:23.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:23.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:23.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:23.636][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-04-10 19:21:23.637][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:21:23.639][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.640][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.641][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:21:23.643][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.644][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.645][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.645][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.646][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:21:23.647][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:21:23.648][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.649][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-04-10 19:21:23.650][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:21:23.651][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-04-10 19:21:23.651][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-04-10 19:21:23.651][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-04-10 19:21:23.651][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-04-10 19:21:23.651][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-04-10 19:21:23.651][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-04-10 19:21:23.651][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-04-10 19:21:23.651][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-04-10 19:21:23.651][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-04-10 19:21:23.652][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:23.653][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:21:23.653][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:21:23.654][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:21:23.655][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:23.656][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:23.656][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:21:23.657][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:23.658][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:23.659][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:21:23.660][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-10 19:21:23.660][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-04-10 19:21:23.661][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:21:23.662][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:21:23.662][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:23.663][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:23.665][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-04-10 19:21:23.666][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:21:23.669][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:21:23.670][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-04-10 19:21:23.671][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:21:23.673][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-04-10 19:21:23.674][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-10 19:21:23.675][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-10 19:21:23.676][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-04-10 19:21:23.677][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-04-10 19:21:23.678][biodb::testThat]
biodb.INFO [2023-04-10 19:21:23.679][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-04-10 19:21:23.680][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:21:23.681][biodb::testThat]
biodb.DEBUG[2023-04-10 19:21:23.776][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[2023-04-10 19:21:23.780][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:21:23.781][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:21:23.783][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-04-10 19:21:24.437][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2023-04-10 19:21:25.091][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:21:25.096][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-04-10 19:21:25.102][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-04-10 19:21:25.185][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2023-04-10 19:21:25.188][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:21:25.189][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:21:25.202][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-04-10 19:21:25.859][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[2023-04-10 19:21:26.514][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:21:26.519][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-04-10 19:21:26.525][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-04-10 19:21:26.534][biodb::testThat]
biodb.INFO [2023-04-10 19:21:26.535][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-04-10 19:21:26.536][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:21:26.537][biodb::testThat]
biodb.INFO [2023-04-10 19:21:26.561][biodb::testThat]
biodb.INFO [2023-04-10 19:21:26.563][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-04-10 19:21:26.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:21:26.564][biodb::testThat]
biodb.DEBUG[2023-04-10 19:21:26.640][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[2023-04-10 19:21:26.643][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:21:26.644][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:21:26.658][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-04-10 19:21:27.161][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-04-10 19:21:27.655][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:21:27.659][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-04-10 19:21:27.665][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-04-10 19:21:27.742][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-04-10 19:21:27.745][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:21:27.747][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-04-10 19:21:27.748][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:21:27.749][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-04-10 19:21:27.850][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2023-04-10 19:21:27.854][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:21:27.855][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:21:27.857][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-04-10 19:21:28.345][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[2023-04-10 19:21:28.838][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:21:28.843][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-04-10 19:21:28.849][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-04-10 19:21:29.002][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[2023-04-10 19:21:29.005][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:21:29.006][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:21:29.008][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-04-10 19:21:30.365][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-04-10 19:21:33.769][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:21:33.772][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-04-10 19:21:33.778][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-04-10 19:21:33.965][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2023-04-10 19:21:33.969][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:21:33.970][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:21:33.972][private$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[2023-04-10 19:21:35.164][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[2023-04-10 19:21:38.722][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:21:38.726][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-04-10 19:21:38.734][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-04-10 19:21:38.865][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:21:38.867][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-04-10 19:21:38.868][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-04-10 19:21:38.869][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:21:38.870][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:38.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:38.940][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:38.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:38.943][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:38.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-10 19:21:38.948][biodb::testContext]
biodb.INFO [2023-04-10 19:21:38.949][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:21:38.950][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-04-10 19:21:38.951][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-10 19:21:38.952][biodb::testContext]
biodb.INFO [2023-04-10 19:21:38.954][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:21:38.955][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-10 19:21:38.959][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:21:38.961][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-10 19:21:38.962][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-10 19:21:38.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:38.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:38.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:38.966][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-10 19:21:38.967][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-10 19:21:38.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:38.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:38.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:38.971][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-10 19:21:38.972][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-10 19:21:38.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:38.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:38.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:38.976][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-10 19:21:38.977][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-10 19:21:38.978][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-10 19:21:38.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:38.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:38.980][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.DEBUG[2023-04-10 19:21:38.981][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-10 19:21:38.982][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-10 19:21:38.983][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-10 19:21:38.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:38.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:38.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:38.987][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-10 19:21:38.988][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-10 19:21:38.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:38.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:38.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:38.991][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-10 19:21:38.992][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-10 19:21:38.993][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-10 19:21:38.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:38.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:38.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:38.997][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-10 19:21:38.998][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-10 19:21:38.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.001][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-10 19:21:39.002][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-10 19:21:39.003][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-10 19:21:39.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.007][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:21:39.008][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-10 19:21:39.009][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-10 19:21:39.010][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-10 19:21:39.011][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-10 19:21:39.012][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-10 19:21:39.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.015][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-10 19:21:39.016][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-10 19:21:39.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.019][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-10 19:21:39.020][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-10 19:21:39.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.023][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[2023-04-10 19:21:39.024][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-10 19:21:39.025][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-10 19:21:39.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.028][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-10 19:21:39.029][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-10 19:21:39.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.033][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-10 19:21:39.034][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-10 19:21:39.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.037][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-10 19:21:39.038][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-10 19:21:39.044][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-10 19:21:39.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.047][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-10 19:21:39.048][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-10 19:21:39.049][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-10 19:21:39.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.053][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-10 19:21:39.055][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.056][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-10 19:21:39.057][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.058][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:21:39.059][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.060][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.061][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.061][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.062][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:21:39.063][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:21:39.064][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.065][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-10 19:21:39.066][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:21:39.067][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.068][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.069][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:21:39.069][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:21:39.069][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:21:39.069][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:21:39.069][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:21:39.070][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:21:39.071][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:39.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:39.073][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:21:39.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:39.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:39.076][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.077][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.078][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:21:39.078][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:21:39.079][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.080][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.081][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-10 19:21:39.083][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.084][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:21:39.085][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.086][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:21:39.087][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.088][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.089][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.090][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.091][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:21:39.092][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:21:39.105][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.107][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-10 19:21:39.108][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:21:39.109][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.110][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.111][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:21:39.111][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:21:39.111][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-10 19:21:39.111][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-10 19:21:39.111][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-10 19:21:39.112][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:21:39.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:39.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:39.115][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:21:39.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:39.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:39.117][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.118][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.119][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:21:39.120][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:21:39.121][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.122][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.123][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-10 19:21:39.125][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.126][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-10 19:21:39.127][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.128][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:21:39.129][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.130][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.130][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.132][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.132][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:21:39.134][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:21:39.135][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.136][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-10 19:21:39.137][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:21:39.138][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.139][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.140][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.140][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:21:39.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:39.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:39.143][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:21:39.144][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:39.145][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:39.146][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.147][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.148][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:21:39.148][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:21:39.149][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.150][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.151][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-10 19:21:39.153][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.154][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-10 19:21:39.155][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.156][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:21:39.157][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.158][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.159][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.160][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.161][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-10 19:21:39.162][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:21:39.163][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.164][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-10 19:21:39.165][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:21:39.166][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.167][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.168][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.169][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:21:39.169][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:39.170][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:39.171][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:21:39.172][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:39.173][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:39.174][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.175][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.176][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:21:39.177][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:21:39.178][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.179][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.180][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:21:39.181][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.182][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[2023-04-10 19:21:39.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.186][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[2023-04-10 19:21:39.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.190][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[2023-04-10 19:21:39.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.267][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-10 19:21:39.268][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-10 19:21:39.269][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-10 19:21:39.271][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-10 19:21:39.272][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-10 19:21:39.274][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-10 19:21:39.275][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-10 19:21:39.276][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-10 19:21:39.278][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-10 19:21:39.279][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-10 19:21:39.280][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-10 19:21:39.282][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-10 19:21:39.283][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-10 19:21:39.284][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-10 19:21:39.285][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-10 19:21:39.287][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:21:39.288][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-10 19:21:39.289][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-10 19:21:39.290][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-10 19:21:39.292][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-10 19:21:39.293][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-10 19:21:39.294][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-10 19:21:39.296][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-10 19:21:39.297][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-10 19:21:39.298][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-10 19:21:39.299][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-10 19:21:39.301][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-10 19:21:39.302][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-10 19:21:39.303][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-10 19:21:39.305][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-10 19:21:39.306][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-10 19:21:39.307][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-10 19:21:39.308][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-10 19:21:39.310][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-10 19:21:39.311][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-10 19:21:39.312][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-10 19:21:39.313][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-10 19:21:39.315][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-10 19:21:39.316][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-10 19:21:39.317][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-10 19:21:39.318][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-10 19:21:39.320][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-10 19:21:39.321][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-10 19:21:39.322][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-10 19:21:39.324][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-10 19:21:39.325][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-10 19:21:39.326][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-10 19:21:39.327][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-10 19:21:39.329][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-10 19:21:39.330][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-10 19:21:39.331][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-10 19:21:39.332][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-10 19:21:39.334][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-10 19:21:39.335][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-10 19:21:39.336][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-10 19:21:39.338][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-10 19:21:39.339][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-10 19:21:39.340][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-10 19:21:39.341][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-10 19:21:39.343][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-10 19:21:39.344][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-10 19:21:39.345][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-10 19:21:39.347][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-10 19:21:39.348][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-10 19:21:39.349][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-10 19:21:39.350][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-10 19:21:39.352][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-10 19:21:39.353][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-10 19:21:39.354][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-10 19:21:39.356][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-10 19:21:39.357][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-10 19:21:39.358][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-10 19:21:39.360][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-10 19:21:39.361][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-10 19:21:39.362][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-10 19:21:39.364][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-10 19:21:39.365][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-10 19:21:39.366][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-10 19:21:39.368][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-10 19:21:39.369][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-10 19:21:39.371][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-10 19:21:39.372][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-10 19:21:39.373][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-10 19:21:39.375][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-10 19:21:39.376][initialize] This is biodb version 1.6.1.
biodb.DEBUG[2023-04-10 19:21:39.377][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-10 19:21:39.378][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.380][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-10 19:21:39.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:39.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:39.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:39.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:39.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:39.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:39.497][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.16-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-04-10 19:21:39.498][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:21:39.500][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.501][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.502][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.503][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-10 19:21:39.504][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.505][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.505][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.506][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.507][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-10 19:21:39.508][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-10 19:21:39.509][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.510][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-04-10 19:21:39.511][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-10 19:21:39.512][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-04-10 19:21:39.512][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-04-10 19:21:39.512][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-04-10 19:21:39.512][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-04-10 19:21:39.512][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-04-10 19:21:39.512][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-04-10 19:21:39.512][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-04-10 19:21:39.512][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-04-10 19:21:39.512][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-04-10 19:21:39.513][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-10 19:21:39.514][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-10 19:21:39.514][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-10 19:21:39.515][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-10 19:21:39.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:39.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:39.518][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-10 19:21:39.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-10 19:21:39.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-10 19:21:39.520][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-10 19:21:39.521][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-10 19:21:39.521][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-04-10 19:21:39.522][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-10 19:21:39.523][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-10 19:21:39.524][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-10 19:21:39.525][self$setPropertyValue]
biodb.DEBUG[2023-04-10 19:21:39.526][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-04-10 19:21:39.528][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-10 19:21:39.531][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:21:39.532][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-04-10 19:21:39.533][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-04-10 19:21:39.535][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-04-10 19:21:39.536][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-10 19:21:39.537][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-10 19:21:39.538][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-04-10 19:21:39.539][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-04-10 19:21:39.541][biodb::testThat]
biodb.INFO [2023-04-10 19:21:39.542][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2023-04-10 19:21:39.543][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-10 19:21:39.544][biodb::testThat]
biodb.DEBUG[2023-04-10 19:21:39.644][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[2023-04-10 19:21:39.649][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-10 19:21:39.651][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-04-10 19:21:39.652][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-10 19:21:39.705][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-04-10 19:21:40.570][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-04-10 19:21:40.572][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-10 19:21:40.575][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-04-10 19:21:40.577][cch$loadFileContent] file.exist = [2]: "FALSE, TRUE".
biodb.TRACE[2023-04-10 19:21:40.578][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2023-04-10 19:21:40.580][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-10 19:21:40.581][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-10 19:21:40.582][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-10 19:21:40.583][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-10 19:21:40.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:21:40.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:40.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:40.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:40.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:40.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:40.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-10 19:21:40.598][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2023-04-10 19:21:40.601][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-10 19:21:40.602][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-10 19:21:40.603][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2023-04-10 19:21:41.537][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2023-04-10 19:21:42.475][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-10 19:21:42.479][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2023-04-10 19:21:42.484][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.TRACE[2023-04-10 19:21:42.488][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2023-04-10 19:21:42.490][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-10 19:21:42.491][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-04-10 19:21:42.493][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-10 19:21:42.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:21:42.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:42.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:42.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:42.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:42.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:42.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:21:42.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.527][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:21:42.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:21:42.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.531][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:21:42.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:21:42.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.535][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.539][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.547][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.552][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:21:42.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:42.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.556][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:21:42.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:42.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.560][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:42.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:42.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.565][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:42.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:42.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.578][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:21:42.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.583][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:21:42.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.612][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:21:42.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.636][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.639][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.647][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:21:42.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:21:42.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:42.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:42.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:42.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:42.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:42.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:21:42.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.692][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:21:42.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-10 19:21:42.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.696][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:21:42.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-10 19:21:42.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.700][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.704][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.708][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.712][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.716][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:21:42.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:42.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.720][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-10 19:21:42.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:42.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.724][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:42.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:42.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.728][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:42.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:42.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.736][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.740][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:21:42.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.744][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-10 19:21:42.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.764][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.768][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-10 19:21:42.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.772][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.775][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.783][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-10 19:21:42.819][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-04-10 19:21:42.821][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-10 19:21:42.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:21:42.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:42.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:42.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:42.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:42.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:42.832][FUN] Functions in observer BiodbConfig: [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[2023-04-10 19:21:42.834][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:21:42.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:21:42.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.838][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:21:42.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:21:42.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.841][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:21:42.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:21:42.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.845][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:21:42.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:21:42.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.849][private$selectFields] Fields none
biodb.TRACE[2023-04-10 19:21:42.850][private$selectFields]
biodb.TRACE[2023-04-10 19:21:42.850][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-04-10 19:21:42.851][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:21:42.852][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:21:42.853][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.854][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.855][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.856][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.857][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.858][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.859][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.860][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.860][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.861][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.862][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.863][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.864][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.865][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.866][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.867][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.868][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:42.869][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:42.870][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.870][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.871][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:42.872][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:42.873][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.874][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.875][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.876][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.877][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.878][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.879][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.880][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.881][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.882][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.883][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.884][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.885][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.885][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.886][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.887][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.900][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.902][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.903][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.904][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.905][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.906][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.907][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.908][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.909][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.909][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.910][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:42.911][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:42.912][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.913][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.914][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:42.915][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:42.916][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.917][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.918][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.919][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.920][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.921][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.922][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.923][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.924][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.924][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.925][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:21:42.926][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:21:42.927][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.928][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.929][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.930][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.931][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.932][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.933][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.934][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.935][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.936][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.937][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.937][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.938][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.939][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.940][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.941][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.942][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:42.943][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:42.944][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.945][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.946][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:42.947][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:42.948][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.949][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.950][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:42.951][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:42.952][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.952][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.953][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.954][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:42.955][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.956][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.957][private$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[2023-04-10 19:21:42.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:42.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:42.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:42.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.981][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.985][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.989][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:42.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.993][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:42.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:42.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:42.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.000][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.016][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:43.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:43.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.020][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:43.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:43.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.024][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:43.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:43.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:43.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:43.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:43.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:43.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:43.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:43.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.052][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.056][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.059][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.069][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2023-04-10 19:21:43.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-10 19:21:43.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:43.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:43.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:43.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:43.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:43.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-10 19:21:43.082][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:21:43.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:21:43.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.086][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-10 19:21:43.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-10 19:21:43.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.090][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-10 19:21:43.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-10 19:21:43.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.093][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-10 19:21:43.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-10 19:21:43.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.097][private$selectFields] Fields none
biodb.TRACE[2023-04-10 19:21:43.098][private$selectFields]
biodb.TRACE[2023-04-10 19:21:43.099][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-04-10 19:21:43.100][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-10 19:21:43.101][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:21:43.102][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:43.103][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:43.104][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.105][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.105][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:43.106][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:43.107][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.108][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.109][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:43.110][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:43.111][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.112][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.113][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.114][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.115][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.115][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.116][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.117][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.118][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.119][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.120][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:43.121][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:43.122][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.123][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.124][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:43.125][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:43.126][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.126][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.127][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.128][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.129][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.130][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.131][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:43.132][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:43.133][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.134][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.135][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:43.136][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:43.136][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.137][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.138][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:43.139][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:43.140][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.141][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.142][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.143][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.144][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.145][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.146][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.147][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.147][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.148][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.149][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:43.150][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:43.151][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.152][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.153][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:43.154][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:43.155][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.156][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.157][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.158][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.159][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.160][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.161][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:21:43.161][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-10 19:21:43.162][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:43.163][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:43.164][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.165][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.166][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:43.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:43.168][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.169][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.170][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:43.171][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:43.172][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.173][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.174][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.175][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.176][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.177][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.177][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.192][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.193][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.194][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.195][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:43.196][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:43.197][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.198][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.198][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:43.200][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:43.200][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.201][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.202][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.203][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.204][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.205][ef$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.206][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-04-10 19:21:43.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:43.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:43.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:43.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:43.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-10 19:21:43.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-10 19:21:43.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:43.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:43.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:43.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:43.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-10 19:21:43.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-10 19:21:43.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.230][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:43.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:43.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.233][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:43.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:43.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.237][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:43.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-10 19:21:43.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.241][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.245][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.248][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-10 19:21:43.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-10 19:21:43.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.263][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:43.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:43.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.267][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:43.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:43.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.271][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-10 19:21:43.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-10 19:21:43.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:43.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:43.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:43.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:43.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.283][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-10 19:21:43.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-10 19:21:43.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.287][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.291][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.295][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-10 19:21:43.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-10 19:21:43.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-10 19:21:43.303][private$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[2023-04-10 19:21:43.304][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-10 19:21:43.305][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-04-10 19:21:43.308][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-10 19:21:43.309][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-04-10 19:21:43.310][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-04-10 19:21:43.311][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-10 19:21:43.312][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-10 19:21:43.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-10 19:21:43.314][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-10 19:21:43.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-10 19:21:43.315][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-10 19:21:43.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 169 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 169 ]
> 
> proc.time()
   user  system elapsed 
 19.872   1.867 133.795

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn1.7840.1221.907
LipidmapsStructureEntry0.2950.0040.299