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This page was generated on 2023-02-08 01:14:53 -0000 (Wed, 08 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4164
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CHECK results for biodbLipidmaps on kunpeng1


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 183/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.5.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-02-06 00:12:45 -0000 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: master
git_last_commit: f341783
git_last_commit_date: 2022-12-01 12:24:56 -0000 (Thu, 01 Dec 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: biodbLipidmaps
Version: 1.5.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings biodbLipidmaps_1.5.0.tar.gz
StartedAt: 2023-02-06 19:01:03 -0000 (Mon, 06 Feb 2023)
EndedAt: 2023-02-06 19:05:04 -0000 (Mon, 06 Feb 2023)
EllapsedTime: 241.3 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings biodbLipidmaps_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbLipidmaps.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
LipidmapsStructureConn 2.802  0.204   5.625
* 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-3.17-bioc/R/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 [2023-02-06 19:01:56.704][biodb::testContext]
biodb.INFO [2023-02-06 19:01:56.707][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:01:56.708][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-02-06 19:01:56.710][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:01:56.711][biodb::testContext]
biodb.INFO [2023-02-06 19:01:56.732][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:01:56.735][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-06 19:01:56.745][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:01:56.746][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-06 19:01:56.748][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-06 19:01:56.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.754][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-06 19:01:56.782][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-06 19:01:56.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.787][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-06 19:01:56.789][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-06 19:01:56.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.794][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-06 19:01:56.796][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-06 19:01:56.797][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-06 19:01:56.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.803][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-06 19:01:56.804][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-06 19:01:56.806][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-06 19:01:56.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.812][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-06 19:01:56.813][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-06 19:01:56.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.819][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-06 19:01:56.820][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-06 19:01:56.822][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-06 19:01:56.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.828][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-06 19:01:56.829][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-06 19:01:56.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.835][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-06 19:01:56.836][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-06 19:01:56.838][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-06 19:01:56.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.844][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:01:56.845][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-06 19:01:56.847][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-06 19:01:56.848][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-06 19:01:56.850][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-06 19:01:56.851][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-06 19:01:56.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.857][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-06 19:01:56.859][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-06 19:01:56.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.864][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-06 19:01:56.866][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-06 19:01:56.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.870][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[2023-02-06 19:01:56.872][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-06 19:01:56.873][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-06 19:01:56.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.879][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-06 19:01:56.880][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-06 19:01:56.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.886][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-06 19:01:56.888][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-06 19:01:56.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.893][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:01:56.895][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-06 19:01:56.899][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-06 19:01:56.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.905][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-06 19:01:56.907][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-06 19:01:56.908][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-06 19:01:56.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:56.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:56.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:56.918][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-06 19:01:56.979][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.002][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-02-06 19:01:57.003][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.005][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:57.006][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.008][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.009][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.010][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.012][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:01:57.013][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:57.015][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.016][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-06 19:01:57.017][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:57.019][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.020][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.021][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:01:57.021][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:01:57.021][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:01:57.021][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:01:57.021][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:01:57.023][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:57.024][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:57.025][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:57.027][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:57.028][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:57.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:57.031][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.032][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.033][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:57.034][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:57.036][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.037][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.039][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-06 19:01:57.041][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.043][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:01:57.044][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.045][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:57.047][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.048][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.049][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.051][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.052][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:01:57.053][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:57.055][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.056][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-06 19:01:57.058][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:57.059][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.060][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.062][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:01:57.062][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:01:57.062][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:01:57.062][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:01:57.062][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:01:57.063][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:57.065][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:57.066][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:57.067][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:57.069][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:57.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:57.071][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.073][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.074][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:57.075][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:57.077][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.078][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.080][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-06 19:01:57.082][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.083][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-02-06 19:01:57.085][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.086][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:57.088][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.089][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.090][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.092][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.093][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:01:57.094][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:57.096][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.097][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-06 19:01:57.099][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:57.100][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.102][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.103][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.104][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:57.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:57.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:57.108][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:57.110][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:57.111][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:57.112][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.114][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.115][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:57.116][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:57.118][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.119][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.121][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-06 19:01:57.123][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.125][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:01:57.126][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.128][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:57.129][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.131][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.132][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.133][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.135][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:01:57.136][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:57.138][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.139][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-06 19:01:57.140][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:57.142][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.143][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.145][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.146][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:57.148][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:57.149][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:57.150][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:57.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:57.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:57.154][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.156][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.157][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:57.158][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:57.160][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.161][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.166][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:01:57.168][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.182][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[2023-02-06 19:01:57.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.194][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[2023-02-06 19:01:57.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.207][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[2023-02-06 19:01:57.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.266][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[2023-02-06 19:01:57.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.287][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-06 19:01:57.294][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-06 19:01:57.296][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-06 19:01:57.298][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-06 19:01:57.300][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:01:57.302][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:01:57.304][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-06 19:01:57.306][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-06 19:01:57.308][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-06 19:01:57.310][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:01:57.312][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:01:57.314][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-06 19:01:57.316][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-06 19:01:57.318][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-06 19:01:57.320][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-06 19:01:57.322][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:01:57.324][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-06 19:01:57.326][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-06 19:01:57.328][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:01:57.330][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-06 19:01:57.332][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-06 19:01:57.334][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-06 19:01:57.336][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-06 19:01:57.338][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-06 19:01:57.340][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-06 19:01:57.342][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-06 19:01:57.344][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-06 19:01:57.346][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-06 19:01:57.348][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-06 19:01:57.350][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-06 19:01:57.352][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-06 19:01:57.354][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-06 19:01:57.356][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-06 19:01:57.358][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-06 19:01:57.360][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-06 19:01:57.362][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-06 19:01:57.364][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-06 19:01:57.366][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-06 19:01:57.368][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-06 19:01:57.370][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-06 19:01:57.373][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-06 19:01:57.375][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-06 19:01:57.377][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-06 19:01:57.379][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-06 19:01:57.381][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-06 19:01:57.383][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-06 19:01:57.385][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-06 19:01:57.387][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-06 19:01:57.389][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-06 19:01:57.391][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-06 19:01:57.393][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-06 19:01:57.395][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-06 19:01:57.397][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-06 19:01:57.400][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-06 19:01:57.402][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-06 19:01:57.404][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-06 19:01:57.406][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-06 19:01:57.408][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-06 19:01:57.410][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-06 19:01:57.412][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-06 19:01:57.414][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-06 19:01:57.416][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-06 19:01:57.418][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-06 19:01:57.420][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-06 19:01:57.422][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-06 19:01:57.424][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-06 19:01:57.427][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:01:57.429][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:01:57.431][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-06 19:01:57.433][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-06 19:01:57.435][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-06 19:01:57.438][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-06 19:01:57.440][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-06 19:01:57.442][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-06 19:01:57.444][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-06 19:01:57.446][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-06 19:01:57.449][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-06 19:01:57.451][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-06 19:01:57.453][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-06 19:01:57.455][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-06 19:01:57.457][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-06 19:01:57.459][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-06 19:01:57.461][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-06 19:01:57.469][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-06 19:01:57.471][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:01:57.475][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:01:57.477][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.479][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.495][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[2023-02-06 19:01:57.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.539][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[2023-02-06 19:01:57.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.548][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[2023-02-06 19:01:57.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.557][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[2023-02-06 19:01:57.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.582][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[2023-02-06 19:01:57.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.609][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[2023-02-06 19:01:57.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.617][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[2023-02-06 19:01:57.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:01:57.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:01:57.647][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-02-06 19:01:57.660][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-02-06 19:01:57.663][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.664][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.665][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.667][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:01:57.668][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.670][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.671][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.672][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.674][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:01:57.675][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:01:57.676][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.678][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-02-06 19:01:57.679][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:01:57.681][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-02-06 19:01:57.681][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-02-06 19:01:57.681][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-02-06 19:01:57.681][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-02-06 19:01:57.681][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-02-06 19:01:57.681][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-02-06 19:01:57.681][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-02-06 19:01:57.681][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-02-06 19:01:57.681][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-02-06 19:01:57.682][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-06 19:01:57.683][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:01:57.683][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:01:57.685][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:01:57.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:57.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:57.689][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:01:57.690][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:01:57.691][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:01:57.693][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:01:57.694][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-02-06 19:01:57.694][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-02-06 19:01:57.695][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:01:57.697][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:01:57.698][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-06 19:01:57.699][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:01:57.707][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-02-06 19:01:57.710][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:01:57.740][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-02-06 19:01:57.742][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-02-06 19:01:57.748][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-02-06 19:01:57.753][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-02-06 19:01:57.759][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-02-06 19:01:57.760][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-02-06 19:01:57.762][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-02-06 19:01:57.764][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-02-06 19:01:57.785][biodb::testThat]
biodb.INFO [2023-02-06 19:01:57.787][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-02-06 19:01:57.788][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:57.790][biodb::testThat]
biodb.TRACE[2023-02-06 19:01:57.795][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-02-06 19:01:57.801][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:57.806][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-02-06 19:01:57.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:57.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:57.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:57.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:57.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:57.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:57.841][FUN] Functions in observer BiodbConfig: [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[2023-02-06 19:01:57.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:57.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:57.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:57.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:57.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:57.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:57.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.895][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:57.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:57.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.901][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:57.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:57.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.906][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:57.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:57.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.961][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:57.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:57.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.971][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:57.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:57.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.976][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:57.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:57.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.986][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:01:57.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:57.992][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:01:57.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:57.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:57.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.002][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:58.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:58.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.008][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:58.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:58.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.024][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.033][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:01:58.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.039][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-06 19:01:58.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.057][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:01:58.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.211][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.217][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.229][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:58.274][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-02-06 19:01:58.281][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:01:58.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:01:58.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.287][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:01:58.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:01:58.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.293][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-06 19:01:58.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-06 19:01:58.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.298][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-06 19:01:58.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-06 19:01:58.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.347][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.396][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.402][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.407][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:58.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.440][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.442][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.443][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.444][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.461][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.477][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.479][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.481][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.507][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.513][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.519][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.524][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.526][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.527][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.529][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.530][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.546][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:58.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:58.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.551][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:58.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:58.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.557][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:58.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:58.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.562][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:58.564][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:58.565][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.567][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:58.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:58.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.600][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.602][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.603][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.604][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.621][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.627][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.633][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.638][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.640][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.641][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.643][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.644][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.660][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.662][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.663][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.664][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.672][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.673][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.675][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.676][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.684][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:58.685][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:58.687][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.688][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.696][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.698][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.699][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.700][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.708][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.710][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.711][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.713][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.720][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.722][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.723][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.725][ef$get] fields variable is a list.
biodb.INFO [2023-02-06 19:01:58.734][biodb::testThat]
biodb.INFO [2023-02-06 19:01:58.735][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-02-06 19:01:58.736][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:58.738][biodb::testThat]
biodb.DEBUG[2023-02-06 19:01:58.757][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-02-06 19:01:58.774][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:01:58.780][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-02-06 19:01:58.782][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:01:58.784][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-02-06 19:01:58.786][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:01:58.846][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:01:58.848][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-02-06 19:01:58.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:01:58.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:01:58.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:01:58.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:01:58.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:01:58.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:01:58.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:01:58.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:58.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:58.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:58.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:58.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:01:58.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:01:58.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.901][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:58.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:01:58.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.906][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:58.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:01:58.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.912][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.918][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:01:58.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.927][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.933][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:01:58.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.942][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:01:58.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.948][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:01:58.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:01:58.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.957][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:58.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:58.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.963][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:01:58.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:01:58.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:58.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.988][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:01:58.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.994][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-06 19:01:58.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:58.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:58.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:58.999][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:59.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:59.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:59.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:59.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.011][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:01:59.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:59.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:59.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:59.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:59.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:59.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:59.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:59.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:59.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:59.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:59.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:59.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.061][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:59.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:59.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.068][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:59.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:59.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:59.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:59.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.079][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:59.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:01:59.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:59.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:59.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:59.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:59.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:59.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:59.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:59.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:59.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:59.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:59.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:01:59.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:01:59.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:59.122][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-02-06 19:01:59.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-02-06 19:01:59.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-02-06 19:01:59.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-02-06 19:01:59.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-02-06 19:01:59.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-02-06 19:01:59.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-02-06 19:01:59.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:01:59.148][biodb::testThat]
biodb.INFO [2023-02-06 19:01:59.150][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-02-06 19:01:59.151][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:01:59.152][biodb::testThat]
biodb.TRACE[2023-02-06 19:01:59.156][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:59.157][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:59.159][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.160][ef$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:59.161][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-02-06 19:01:59.200][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:59.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:59.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:59.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:59.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:01:59.210][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:01:59.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:01:59.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:01:59.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:01:59.218][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-02-06 19:01:59.235][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[2023-02-06 19:01:59.264][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:01:59.265][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:01:59.267][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-02-06 19:02:00.404][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-02-06 19:02:02.259][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:02.270][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-02-06 19:02:02.301][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-02-06 19:02:02.308][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-02-06 19:02:02.347][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:02.349][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:02.350][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.351][ef$get] fields variable is a list.
biodb.INFO [2023-02-06 19:02:02.354][biodb::testThat]
biodb.INFO [2023-02-06 19:02:02.355][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-02-06 19:02:02.357][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:02.358][biodb::testThat]
biodb.TRACE[2023-02-06 19:02:02.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:02.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:02.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:02.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:02.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:02.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:02.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:02.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:02.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:02.576][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-02-06 19:02:02.580][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:02.602][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-02-06 19:02:02.604][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:02.606][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-02-06 19:02:02.628][biodb::testThat]
biodb.INFO [2023-02-06 19:02:02.629][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-02-06 19:02:02.631][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:02.632][biodb::testThat]
biodb.TRACE[2023-02-06 19:02:02.667][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:02:02.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:02:02.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:02.673][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:02:02.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:02:02.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:02.678][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-06 19:02:02.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-06 19:02:02.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:02.684][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-06 19:02:02.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-06 19:02:02.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:02.758][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:02:02.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:02:02.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:02.763][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:02:02.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:02:02.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:02.769][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-06 19:02:02.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-06 19:02:02.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:02.774][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-06 19:02:02.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-06 19:02:02.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:02.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:02:02.782][biodb::testThat]
biodb.INFO [2023-02-06 19:02:02.784][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-02-06 19:02:02.785][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:02.787][biodb::testThat]
biodb.INFO [2023-02-06 19:02:02.794][biodb::testThat]
biodb.INFO [2023-02-06 19:02:02.795][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-02-06 19:02:02.797][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:02.798][biodb::testThat]
biodb.INFO [2023-02-06 19:02:02.804][biodb::testThat]
biodb.INFO [2023-02-06 19:02:02.805][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-02-06 19:02:02.806][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:02.808][biodb::testThat]
biodb.DEBUG[2023-02-06 19:02:02.812][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-02-06 19:02:04.032][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-02-06 19:02:04.756][biodb::testThat]
biodb.INFO [2023-02-06 19:02:04.758][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-02-06 19:02:04.759][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:04.760][biodb::testThat]
biodb.TRACE[2023-02-06 19:02:04.772][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:04.774][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:04.775][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.777][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.778][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:04.779][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:04.781][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.782][ef$get] fields variable is a list.
biodb.INFO [2023-02-06 19:02:04.784][biodb::testThat]
biodb.INFO [2023-02-06 19:02:04.786][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-02-06 19:02:04.787][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:04.788][biodb::testThat]
biodb.TRACE[2023-02-06 19:02:04.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:04.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:04.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.818][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:04.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:04.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:04.823][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:04.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:04.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:04.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:04.956][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-02-06 19:02:04.960][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:04.962][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-02-06 19:02:04.964][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:04.966][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-02-06 19:02:05.081][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-02-06 19:02:05.085][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:02:05.087][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-02-06 19:02:05.089][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:02:05.091][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-02-06 19:02:05.114][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:02:05.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:02:05.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:05.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:05.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:05.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:05.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:05.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:05.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:05.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:05.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:05.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:05.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:05.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:05.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:05.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:05.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:05.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:05.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:05.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:05.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:05.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:05.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:05.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:05.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:05.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:05.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:05.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:05.231][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-02-06 19:02:05.254][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:05.256][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:05.287][private$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[2023-02-06 19:02:09.665][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[2023-02-06 19:02:19.455][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:19.465][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2023-02-06 19:02:19.510][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2023-02-06 19:02:20.854][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[2023-02-06 19:02:20.859][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:20.861][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:20.864][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2023-02-06 19:02:21.840][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2023-02-06 19:02:22.835][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:22.844][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2023-02-06 19:02:22.860][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2023-02-06 19:02:22.940][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2023-02-06 19:02:22.945][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:22.947][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:22.950][private$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[2023-02-06 19:02:23.903][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[2023-02-06 19:02:24.899][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:24.909][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2023-02-06 19:02:24.926][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2023-02-06 19:02:24.958][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-06 19:02:24.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-06 19:02:24.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:24.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:02:25.012][biodb::testThat]
biodb.INFO [2023-02-06 19:02:25.014][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-02-06 19:02:25.015][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:25.016][biodb::testThat]
biodb.TRACE[2023-02-06 19:02:25.021][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:02:25.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:02:25.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:25.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:25.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:25.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:25.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:25.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:25.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:25.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:25.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:25.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:25.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:25.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:25.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:25.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:25.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:25.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:25.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:25.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:25.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:25.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:25.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:25.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:25.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:25.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:25.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:25.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:25.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:25.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:25.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:25.130][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[2023-02-06 19:02:25.135][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:25.136][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:25.139][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2023-02-06 19:02:29.589][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2023-02-06 19:02:39.171][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:39.181][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-02-06 19:02:39.224][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-02-06 19:02:40.376][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-02-06 19:02:40.438][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-02-06 19:02:40.441][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-02-06 19:02:40.443][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-02-06 19:02:40.444][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:02:40.446][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:02:40.447][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-02-06 19:02:40.449][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:02:40.450][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:02:40.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:40.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:40.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:40.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:40.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:40.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:40.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:40.485][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-02-06 19:02:40.489][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:40.490][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:40.492][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-02-06 19:02:41.450][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-02-06 19:02:42.437][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:42.447][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-02-06 19:02:42.462][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-02-06 19:02:42.467][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:42.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:42.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:42.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:42.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:42.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:42.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:42.483][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-02-06 19:02:42.486][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:42.487][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:42.489][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-02-06 19:02:43.413][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-02-06 19:02:44.396][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:44.405][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-02-06 19:02:44.418][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-02-06 19:02:44.431][private$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[2023-02-06 19:02:44.436][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:02:44.456][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-02-06 19:02:44.458][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-02-06 19:02:44.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:44.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:44.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:44.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:44.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:44.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:44.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:44.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:44.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:44.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:44.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:44.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.540][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:02:44.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:02:44.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.545][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:44.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:44.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.550][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:02:44.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:02:44.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.556][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:02:44.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:02:44.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.565][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:02:44.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:02:44.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.570][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:02:44.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:02:44.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.579][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:02:44.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:44.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.584][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:02:44.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:44.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.593][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:02:44.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:02:44.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.598][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:02:44.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:02:44.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:44.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.612][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:44.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.621][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:02:44.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.626][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-06 19:02:44.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.632][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:44.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.637][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:44.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.642][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:02:44.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.651][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:44.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:44.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.657][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:44.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:44.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.667][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:44.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:44.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:44.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:44.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:44.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:44.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:44.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:44.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:44.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:44.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:02:44.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:02:44.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.776][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:02:44.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:02:44.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.781][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:44.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:02:44.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.787][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:02:44.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:02:44.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.792][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:02:44.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:02:44.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.801][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:02:44.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:02:44.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.807][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:02:44.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:02:44.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.816][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:02:44.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:44.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.821][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:02:44.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:44.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.830][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:02:44.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:02:44.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.836][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:02:44.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:02:44.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:44.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:44.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.879][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:02:44.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.885][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-06 19:02:44.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.890][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:44.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:02:44.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.901][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:02:44.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:02:44.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.910][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:44.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:44.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.915][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:44.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:44.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.926][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:44.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:44.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:44.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:02:44.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:02:44.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:44.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:44.984][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-02-06 19:02:44.997][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-06 19:02:44.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:45.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:45.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:45.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:45.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:45.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:45.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:45.014][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.020][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.025][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:02:45.026][private$selectFields]
biodb.TRACE[2023-02-06 19:02:45.028][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:45.029][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:45.030][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:02:45.032][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.033][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.034][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.036][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.037][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.038][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.040][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.041][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.042][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:02:45.044][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:02:45.045][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.046][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.048][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.049][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.050][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-06 19:02:45.052][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.057][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.080][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-02-06 19:02:45.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:45.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:45.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:45.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:45.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:45.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:45.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:45.098][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.103][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.109][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:02:45.110][private$selectFields]
biodb.TRACE[2023-02-06 19:02:45.111][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:45.113][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:45.114][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:02:45.115][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.117][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.118][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.119][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.121][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.122][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.124][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.125][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.126][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:02:45.128][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:02:45.129][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.130][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.132][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.133][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.134][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-06 19:02:45.136][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.141][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.147][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.153][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-02-06 19:02:45.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:45.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:45.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:45.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:45.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:45.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:45.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:02:45.170][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.175][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.181][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:02:45.182][private$selectFields]
biodb.TRACE[2023-02-06 19:02:45.183][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:02:45.184][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:02:45.186][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:02:45.187][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.189][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.190][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.191][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.193][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.194][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.195][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.197][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.198][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:02:45.199][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:02:45.201][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.202][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.203][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.205][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.206][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-06 19:02:45.208][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.213][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.219][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:02:45.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.225][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-02-06 19:02:45.226][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-02-06 19:02:45.227][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-06 19:02:45.239][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-06 19:02:45.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-06 19:02:45.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:02:45.266][biodb::testThat]
biodb.INFO [2023-02-06 19:02:45.267][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-02-06 19:02:45.268][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:02:45.270][biodb::testThat]
biodb.TRACE[2023-02-06 19:02:45.274][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:02:45.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:02:45.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:45.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:02:45.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:45.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:45.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:45.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:45.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:45.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:45.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:02:45.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:45.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:02:45.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:02:45.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:02:45.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:02:45.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:02:45.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:02:45.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:02:45.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:02:45.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:02:45.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:02:45.451][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[2023-02-06 19:02:45.479][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:02:45.480][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:02:45.483][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2023-02-06 19:02:49.797][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2023-02-06 19:02:58.828][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:02:58.847][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2023-02-06 19:02:58.889][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2023-02-06 19:02:59.988][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-06 19:03:00.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:00.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:00.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:00.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:00.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:00.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:00.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:03:00.053][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.064][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.097][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:00.099][private$selectFields]
biodb.TRACE[2023-02-06 19:03:00.100][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:03:00.101][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:03:00.102][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:00.104][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.105][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.107][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.108][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.109][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.111][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.112][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.113][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.114][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:00.129][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:00.130][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.132][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.133][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.134][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.136][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-06 19:03:00.137][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.143][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.148][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.154][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-02-06 19:03:00.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:00.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:00.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:00.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:00.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:00.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:00.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:03:00.172][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.178][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.184][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:00.185][private$selectFields]
biodb.TRACE[2023-02-06 19:03:00.186][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:03:00.188][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:03:00.189][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:00.191][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.192][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.194][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.195][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.197][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.198][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.200][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.201][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.203][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:00.204][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:00.206][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.207][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.209][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.210][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.211][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-06 19:03:00.213][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.219][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.224][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.230][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-02-06 19:03:00.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:00.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:00.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:00.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:00.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:00.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:00.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:03:00.248][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.253][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.259][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:00.260][private$selectFields]
biodb.TRACE[2023-02-06 19:03:00.262][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:03:00.263][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:03:00.264][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:00.266][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.267][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.269][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.270][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.272][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.273][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.274][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.276][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.277][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:00.279][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:00.280][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.281][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.283][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.284][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.286][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-06 19:03:00.287][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.293][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.298][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:00.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.305][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-02-06 19:03:00.306][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-02-06 19:03:00.338][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-06 19:03:00.350][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-06 19:03:00.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-06 19:03:00.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:03:00.357][biodb::testThat]
biodb.INFO [2023-02-06 19:03:00.358][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-02-06 19:03:00.359][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:03:00.361][biodb::testThat]
biodb.TRACE[2023-02-06 19:03:00.365][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-02-06 19:03:00.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-02-06 19:03:00.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-02-06 19:03:00.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-02-06 19:03:00.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:03:00.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:03:00.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:03:00.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:03:00.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:03:00.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:03:00.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:00.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:03:00.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:03:00.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:00.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:03:00.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:00.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:00.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:00.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:00.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:00.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:00.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:03:00.480][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-02-06 19:03:00.485][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:03:00.487][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-02-06 19:03:00.489][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:03:00.582][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-02-06 19:03:01.681][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-06 19:03:01.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:01.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:01.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:01.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:01.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:01.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:01.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:03:01.699][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.705][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.710][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:01.711][private$selectFields]
biodb.TRACE[2023-02-06 19:03:01.713][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:03:01.714][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:03:01.715][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:01.717][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.718][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.719][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.721][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.722][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.723][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.725][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.726][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.727][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:01.729][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:01.730][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.731][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.733][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.734][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.735][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-06 19:03:01.737][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.742][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.748][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.754][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-02-06 19:03:01.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:01.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:01.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:01.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:01.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:01.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:01.769][FUN] Functions in observer BiodbConfig: [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[2023-02-06 19:03:01.771][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.776][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.782][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:01.783][private$selectFields]
biodb.TRACE[2023-02-06 19:03:01.784][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:03:01.786][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:03:01.787][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:01.788][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.790][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.791][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.792][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.794][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.795][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.797][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.798][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.799][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:01.801][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:01.802][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.804][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.805][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.806][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.808][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-06 19:03:01.809][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.815][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.820][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.826][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-02-06 19:03:01.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:01.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:01.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:01.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:01.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:01.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:01.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:03:01.844][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.849][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.854][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:01.855][private$selectFields]
biodb.TRACE[2023-02-06 19:03:01.857][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-02-06 19:03:01.858][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:03:01.859][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:01.861][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.862][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.863][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.864][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.866][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.867][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.868][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.870][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.871][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:01.872][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:03:01.874][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.875][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.876][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.878][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.879][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-02-06 19:03:01.880][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.886][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.891][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:01.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:01.897][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-02-06 19:03:01.898][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-02-06 19:03:01.900][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-02-06 19:03:01.929][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-02-06 19:03:01.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-02-06 19:03:01.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:01.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-02-06 19:03:01.936][biodb::testThat]
biodb.INFO [2023-02-06 19:03:01.937][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-02-06 19:03:01.938][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:03:01.940][biodb::testThat]
biodb.DEBUG[2023-02-06 19:03:01.943][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-02-06 19:03:01.944][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-02-06 19:03:01.946][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-02-06 19:03:01.948][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-02-06 19:03:01.950][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:03:01.951][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:03:01.953][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-02-06 19:03:01.954][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:03:01.956][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:03:01.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:01.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:01.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:01.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:01.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:01.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:01.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:03:01.991][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-02-06 19:03:01.994][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:01.996][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:01.998][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-06 19:03:02.938][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:02.939][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:02.940][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-06 19:03:02.942][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-06 19:03:04.086][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-06 19:03:04.087][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:04.089][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:04.091][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-06 19:03:05.046][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:05.048][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:05.049][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-06 19:03:05.051][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-06 19:03:06.209][private$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[2023-02-06 19:03:06.211][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:06.212][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:06.214][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-06 19:03:07.142][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:07.144][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:07.145][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-06 19:03:07.146][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-06 19:03:08.296][private$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[2023-02-06 19:03:08.297][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:08.298][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:08.300][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-06 19:03:09.205][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:09.207][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:09.208][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-06 19:03:09.210][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-06 19:03:10.358][private$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[2023-02-06 19:03:10.360][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:10.361][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:10.363][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-06 19:03:11.307][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:11.308][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:11.309][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-06 19:03:11.310][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-06 19:03:12.457][private$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[2023-02-06 19:03:12.459][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:12.460][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:12.462][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-06 19:03:13.356][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:13.357][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:13.359][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-06 19:03:13.360][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-06 19:03:14.508][private$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[2023-02-06 19:03:14.509][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:14.510][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:14.512][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-06 19:03:15.461][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:15.462][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:15.463][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-06 19:03:15.465][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-06 19:03:16.611][private$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[2023-02-06 19:03:16.612][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:16.614][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:16.615][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-06 19:03:17.560][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:17.562][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:17.563][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-06 19:03:17.564][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-06 19:03:18.717][private$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[2023-02-06 19:03:18.718][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:18.719][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:18.721][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-06 19:03:19.676][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:19.677][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:19.679][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-06 19:03:19.680][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-06 19:03:20.833][private$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[2023-02-06 19:03:20.834][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:20.836][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:20.837][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-02-06 19:03:21.771][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:21.773][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:21.774][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-06 19:03:21.776][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-02-06 19:03:23.067][private$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[2023-02-06 19:03:23.077][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-02-06 19:03:23.082][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:03:23.101][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-02-06 19:03:23.103][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-02-06 19:03:23.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:23.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:23.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:23.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:23.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:23.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:23.119][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.TRACE[2023-02-06 19:03:23.122][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:23.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:23.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:23.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:23.127][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:23.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:23.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:23.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:23.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:23.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:23.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:23.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:23.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:23.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:23.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:23.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:23.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:23.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:23.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:23.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:23.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:23.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:23.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:23.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:23.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:23.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:23.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:23.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:23.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:23.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:23.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:23.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:03:23.166][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-02-06 19:03:23.168][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-02-06 19:03:23.176][biodb::testThat]
biodb.INFO [2023-02-06 19:03:23.177][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-02-06 19:03:23.179][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:03:23.180][biodb::testThat]
biodb.DEBUG[2023-02-06 19:03:23.190][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-02-06 19:03:23.192][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-02-06 19:03:23.193][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-02-06 19:03:23.196][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-02-06 19:03:23.197][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-02-06 19:03:23.199][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-02-06 19:03:23.200][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:03:23.202][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-02-06 19:03:23.203][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-02-06 19:03:23.204][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-02-06 19:03:23.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:23.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:23.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:23.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:23.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:23.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:23.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:03:23.225][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-02-06 19:03:23.229][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:23.231][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:23.232][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-06 19:03:24.157][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:24.158][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:24.159][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[2023-02-06 19:03:24.161][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-06 19:03:25.315][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-06 19:03:25.317][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:25.318][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:25.320][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-06 19:03:26.256][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:26.257][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:26.259][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-02-06 19:03:26.260][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-06 19:03:27.412][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-06 19:03:27.414][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:27.415][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:27.417][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-06 19:03:28.349][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:28.350][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:28.351][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[2023-02-06 19:03:28.353][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-06 19:03:29.504][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-06 19:03:29.505][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:29.506][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:29.508][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-06 19:03:30.470][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:30.471][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:30.473][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[2023-02-06 19:03:30.474][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-06 19:03:31.630][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-06 19:03:31.631][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:31.633][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:31.634][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-06 19:03:32.636][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:32.637][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:32.639][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[2023-02-06 19:03:32.640][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-06 19:03:33.797][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-06 19:03:33.798][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:33.800][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:33.802][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-06 19:03:34.749][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:34.751][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:34.752][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[2023-02-06 19:03:34.753][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-06 19:03:35.910][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-06 19:03:35.911][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:35.912][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:35.914][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-06 19:03:36.838][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:36.839][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:36.841][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[2023-02-06 19:03:36.843][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-06 19:03:37.996][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-06 19:03:37.997][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:37.999][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:38.000][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-06 19:03:38.952][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:38.953][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:38.955][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[2023-02-06 19:03:38.956][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-06 19:03:40.114][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-06 19:03:40.115][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:40.116][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:40.118][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-06 19:03:41.069][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:41.070][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:41.072][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[2023-02-06 19:03:41.073][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-06 19:03:42.228][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-06 19:03:42.230][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:42.231][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:42.233][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-02-06 19:03:43.144][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-02-06 19:03:43.145][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-02-06 19:03:43.147][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[2023-02-06 19:03:43.148][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-02-06 19:03:44.306][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-02-06 19:03:44.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:44.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:44.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:44.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:44.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:44.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:44.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:03:44.323][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-02-06 19:03:44.327][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:44.328][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:44.330][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-02-06 19:03:45.333][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-02-06 19:03:46.329][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:03:46.338][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-02-06 19:03:46.353][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-02-06 19:03:46.367][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2023-02-06 19:03:46.373][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-02-06 19:03:46.439][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-02-06 19:03:46.441][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-02-06 19:03:46.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:46.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:46.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:46.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:46.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:46.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:46.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:03:46.459][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:46.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:46.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.465][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:46.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:46.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:03:46.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:03:46.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:03:46.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:03:46.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:03:46.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:03:46.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:03:46.490][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.TRACE[2023-02-06 19:03:46.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:03:46.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:03:46.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:03:46.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:03:46.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.526][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:03:46.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:03:46.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.532][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:03:46.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:03:46.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.542][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:03:46.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:03:46.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.547][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:03:46.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:03:46.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.557][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:03:46.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:03:46.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.563][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:03:46.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:03:46.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.572][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:03:46.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:03:46.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.578][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:03:46.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:03:46.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.587][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:03:46.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:03:46.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.593][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:03:46.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:03:46.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.602][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:03:46.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:03:46.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.608][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:03:46.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:03:46.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:03:46.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:03:46.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.623][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:03:46.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:03:46.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.633][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:03:46.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:03:46.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.638][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-06 19:03:46.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:03:46.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:03:46.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:03:46.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.650][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:03:46.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:03:46.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.655][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:03:46.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:03:46.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:03:46.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:03:46.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:03:46.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:03:46.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:03:46.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:03:46.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:03:46.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:03:46.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:03:46.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:03:46.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.741][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:46.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:46.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.747][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:46.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:46.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.758][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:46.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:03:46.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:03:46.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:03:46.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:03:46.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:03:46.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:03:46.849][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-02-06 19:03:46.851][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-02-06 19:03:46.852][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-02-06 19:03:46.868][biodb::testThat]
biodb.INFO [2023-02-06 19:03:46.869][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-02-06 19:03:46.871][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:03:46.872][biodb::testThat]
biodb.INFO [2023-02-06 19:03:46.899][biodb::testThat]
biodb.INFO [2023-02-06 19:03:46.900][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-02-06 19:03:46.902][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:03:46.903][biodb::testThat]
biodb.INFO [2023-02-06 19:03:46.913][biodb::testThat]
biodb.INFO [2023-02-06 19:03:46.914][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-02-06 19:03:46.916][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:03:46.917][biodb::testThat]
biodb.DEBUG[2023-02-06 19:03:46.921][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[2023-02-06 19:03:46.949][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:03:46.951][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:03:46.953][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-02-06 19:03:51.326][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-02-06 19:04:00.403][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:04:00.413][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-02-06 19:04:00.459][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-02-06 19:04:01.653][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:01.655][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:01.656][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:01.657][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:01.659][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:01.660][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:01.662][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:01.663][ef$get] fields variable is a list.
biodb.INFO [2023-02-06 19:04:01.665][biodb::testThat]
biodb.INFO [2023-02-06 19:04:01.667][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-02-06 19:04:01.668][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:04:01.670][biodb::testThat]
biodb.ERROR[2023-02-06 19:04:01.690][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-02-06 19:04:01.711][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-02-06 19:04:01.724][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-06 19:04:01.726][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-02-06 19:04:01.727][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-02-06 19:04:01.729][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-06 19:04:01.730][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:01.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:01.732][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:01.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:01.735][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-06 19:04:01.750][biodb::testContext]
biodb.INFO [2023-02-06 19:04:01.751][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:04:01.753][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-02-06 19:04:01.754][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:04:01.755][biodb::testContext]
biodb.INFO [2023-02-06 19:04:01.762][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:04:01.764][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-06 19:04:01.769][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:04:01.770][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-06 19:04:01.772][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-06 19:04:01.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.777][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-06 19:04:01.779][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-06 19:04:01.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.784][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-06 19:04:01.785][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-06 19:04:01.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.791][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-06 19:04:01.792][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-06 19:04:01.793][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-06 19:04:01.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.799][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-06 19:04:01.800][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-06 19:04:01.801][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-06 19:04:01.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.807][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-06 19:04:01.808][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-06 19:04:01.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.813][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-06 19:04:01.815][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-06 19:04:01.816][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-06 19:04:01.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.820][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.DEBUG[2023-02-06 19:04:01.821][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-06 19:04:01.823][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-06 19:04:01.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.828][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-06 19:04:01.829][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-06 19:04:01.831][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-06 19:04:01.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.836][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:04:01.837][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-06 19:04:01.839][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-06 19:04:01.840][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-06 19:04:01.842][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-06 19:04:01.843][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-06 19:04:01.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.848][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-06 19:04:01.850][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-06 19:04:01.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.855][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-06 19:04:01.856][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-06 19:04:01.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.861][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-06 19:04:01.863][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-06 19:04:01.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.866][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[2023-02-06 19:04:01.868][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-06 19:04:01.869][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-06 19:04:01.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.874][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-06 19:04:01.876][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-06 19:04:01.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.881][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:04:01.882][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-06 19:04:01.886][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-06 19:04:01.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:01.892][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-06 19:04:01.893][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-06 19:04:01.894][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-06 19:04:01.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:01.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:01.898][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[2023-02-06 19:04:01.899][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-06 19:04:01.902][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:01.903][self$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[2023-02-06 19:04:01.905][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:01.906][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:04:01.908][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:01.909][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:04:01.910][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:01.912][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:04:01.913][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:04:01.915][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:04:01.916][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:01.917][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-06 19:04:01.919][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:04:01.920][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:01.921][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:01.923][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:04:01.923][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:04:01.923][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:04:01.923][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:04:01.923][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:04:01.924][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:04:01.926][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:01.927][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:01.928][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:04:01.929][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:01.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:01.932][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:04:01.933][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:01.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:04:01.936][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:04:01.937][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:01.939][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:01.940][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-06 19:04:01.943][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:01.944][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:04:01.945][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:01.947][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:04:01.948][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:01.950][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:04:01.951][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:01.952][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:04:01.954][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:04:01.955][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:04:01.957][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:01.958][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-06 19:04:01.960][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:04:01.961][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:01.962][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:01.964][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:04:01.964][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:04:01.964][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:04:01.964][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:04:01.964][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:04:01.965][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:04:01.967][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:01.968][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:01.969][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:04:01.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:01.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:01.973][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:04:01.975][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:01.976][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:04:01.977][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:04:01.979][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:01.980][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:01.982][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-06 19:04:01.984][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:01.985][self$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[2023-02-06 19:04:01.987][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:01.988][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:04:01.990][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:01.991][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:04:01.992][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:01.994][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:04:01.995][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:04:01.997][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:04:01.998][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:01.999][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-06 19:04:02.001][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:04:02.002][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:02.004][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:02.005][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:02.006][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:04:02.008][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:02.009][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:02.010][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:04:02.012][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:02.013][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:02.014][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:04:02.015][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:02.017][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:04:02.018][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:04:02.019][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:02.052][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:02.054][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-06 19:04:02.056][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:02.057][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:04:02.059][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:02.060][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:04:02.062][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:02.063][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:04:02.064][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:02.066][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:04:02.067][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:04:02.069][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:04:02.070][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:02.071][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-06 19:04:02.073][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:04:02.074][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:02.075][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:02.077][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:02.078][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:04:02.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:02.081][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:02.082][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:04:02.084][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:02.085][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:02.087][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:04:02.088][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:02.089][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:04:02.091][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:04:02.092][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:02.094][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:02.095][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:04:02.097][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.098][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[2023-02-06 19:04:02.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.124][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[2023-02-06 19:04:02.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.136][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[2023-02-06 19:04:02.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.142][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[2023-02-06 19:04:02.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.182][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[2023-02-06 19:04:02.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.194][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[2023-02-06 19:04:02.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.207][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[2023-02-06 19:04:02.208][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-06 19:04:02.211][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-06 19:04:02.213][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-06 19:04:02.215][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-06 19:04:02.217][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:04:02.219][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:04:02.220][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-06 19:04:02.222][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-06 19:04:02.224][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-06 19:04:02.226][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:04:02.228][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:04:02.230][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-06 19:04:02.232][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-06 19:04:02.234][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-06 19:04:02.236][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-06 19:04:02.238][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:04:02.240][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-06 19:04:02.242][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-06 19:04:02.244][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:04:02.246][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-06 19:04:02.248][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-06 19:04:02.250][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-06 19:04:02.252][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-06 19:04:02.254][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-06 19:04:02.256][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-06 19:04:02.258][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-06 19:04:02.260][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-06 19:04:02.262][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-06 19:04:02.264][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-06 19:04:02.266][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-06 19:04:02.268][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-06 19:04:02.270][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-06 19:04:02.273][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-06 19:04:02.275][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-06 19:04:02.277][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-06 19:04:02.279][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-06 19:04:02.281][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-06 19:04:02.283][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-06 19:04:02.285][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-06 19:04:02.287][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-06 19:04:02.289][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-06 19:04:02.291][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-06 19:04:02.293][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-06 19:04:02.295][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-06 19:04:02.297][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-06 19:04:02.299][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-06 19:04:02.301][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-06 19:04:02.303][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-06 19:04:02.305][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-06 19:04:02.307][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-06 19:04:02.309][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-06 19:04:02.311][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-06 19:04:02.313][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-06 19:04:02.315][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-06 19:04:02.317][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-06 19:04:02.319][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-06 19:04:02.321][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-06 19:04:02.323][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-06 19:04:02.325][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-06 19:04:02.327][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-06 19:04:02.329][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-06 19:04:02.331][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-06 19:04:02.333][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-06 19:04:02.335][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-06 19:04:02.337][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-06 19:04:02.339][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-06 19:04:02.341][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:04:02.343][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:04:02.345][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-06 19:04:02.347][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-06 19:04:02.349][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-06 19:04:02.351][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-06 19:04:02.353][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-06 19:04:02.356][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-06 19:04:02.358][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-06 19:04:02.360][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-06 19:04:02.362][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-06 19:04:02.364][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-06 19:04:02.366][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-06 19:04:02.368][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-06 19:04:02.370][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-06 19:04:02.372][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-06 19:04:02.374][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-06 19:04:02.376][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-06 19:04:02.378][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:04:02.380][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:04:02.381][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.384][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:02.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:02.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:02.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:02.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:02.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:02.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:02.555][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-02-06 19:04:02.556][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-02-06 19:04:02.559][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:02.560][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-06 19:04:02.562][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:02.563][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:04:02.565][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:02.566][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:04:02.568][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:02.569][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:04:02.570][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:04:02.572][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:04:02.573][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:02.575][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-02-06 19:04:02.576][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:04:02.578][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-02-06 19:04:02.578][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-02-06 19:04:02.578][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-02-06 19:04:02.578][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-02-06 19:04:02.578][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-02-06 19:04:02.578][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-02-06 19:04:02.578][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-02-06 19:04:02.578][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-02-06 19:04:02.578][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-02-06 19:04:02.579][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:02.581][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:04:02.581][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:04:02.582][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:04:02.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:02.585][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:02.586][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:04:02.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:02.589][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:02.591][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:04:02.592][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-02-06 19:04:02.592][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-02-06 19:04:02.594][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:04:02.595][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:04:02.596][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:02.598][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:02.599][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-02-06 19:04:02.602][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:04:02.606][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-02-06 19:04:02.607][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-02-06 19:04:02.609][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-02-06 19:04:02.611][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-02-06 19:04:02.613][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-02-06 19:04:02.614][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-02-06 19:04:02.616][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-02-06 19:04:02.617][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-02-06 19:04:02.619][biodb::testThat]
biodb.INFO [2023-02-06 19:04:02.621][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-02-06 19:04:02.622][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:04:02.623][biodb::testThat]
biodb.DEBUG[2023-02-06 19:04:02.629][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2023-02-06 19:04:02.634][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:04:02.636][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:04:02.638][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-02-06 19:04:03.638][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[2023-02-06 19:04:04.635][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:04:04.644][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-02-06 19:04:04.660][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-02-06 19:04:04.675][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[2023-02-06 19:04:04.680][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:04:04.681][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:04:04.684][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-02-06 19:04:05.684][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2023-02-06 19:04:06.684][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:04:06.694][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-02-06 19:04:06.710][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-02-06 19:04:06.756][biodb::testThat]
biodb.INFO [2023-02-06 19:04:06.757][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-02-06 19:04:06.758][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:04:06.760][biodb::testThat]
biodb.INFO [2023-02-06 19:04:06.793][biodb::testThat]
biodb.INFO [2023-02-06 19:04:06.794][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-02-06 19:04:06.796][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:04:06.797][biodb::testThat]
biodb.DEBUG[2023-02-06 19:04:06.801][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-02-06 19:04:06.806][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:04:06.808][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:04:06.810][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-02-06 19:04:07.650][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-02-06 19:04:08.525][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:04:08.534][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-02-06 19:04:08.548][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-02-06 19:04:08.557][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[2023-02-06 19:04:08.561][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:04:08.563][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-02-06 19:04:08.565][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:04:08.567][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-02-06 19:04:08.573][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[2023-02-06 19:04:08.577][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:04:08.579][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:04:08.581][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-02-06 19:04:09.404][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2023-02-06 19:04:10.203][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:04:10.212][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-02-06 19:04:10.228][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-02-06 19:04:10.238][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2023-02-06 19:04:10.243][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:04:10.244][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:04:10.246][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-02-06 19:04:11.823][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-02-06 19:04:14.131][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:04:14.141][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-02-06 19:04:14.158][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-02-06 19:04:14.311][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[2023-02-06 19:04:14.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-02-06 19:04:14.316][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-02-06 19:04:14.319][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2023-02-06 19:04:15.910][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2023-02-06 19:04:18.087][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-02-06 19:04:18.097][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-02-06 19:04:18.117][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-02-06 19:04:18.265][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-06 19:04:18.266][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-02-06 19:04:18.268][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-02-06 19:04:18.269][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-06 19:04:18.270][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:18.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:18.273][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.275][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-02-06 19:04:18.282][biodb::testContext]
biodb.INFO [2023-02-06 19:04:18.283][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:04:18.285][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-02-06 19:04:18.286][biodb::testContext] ********************************************************************************
biodb.INFO [2023-02-06 19:04:18.288][biodb::testContext]
biodb.INFO [2023-02-06 19:04:18.294][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:04:18.296][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2023-02-06 19:04:18.301][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:04:18.303][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-02-06 19:04:18.304][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-02-06 19:04:18.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.309][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-02-06 19:04:18.311][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-02-06 19:04:18.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.316][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-02-06 19:04:18.318][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-02-06 19:04:18.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.323][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-02-06 19:04:18.324][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-02-06 19:04:18.326][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-02-06 19:04:18.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.331][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-02-06 19:04:18.332][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-02-06 19:04:18.334][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-02-06 19:04:18.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.339][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-02-06 19:04:18.340][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-02-06 19:04:18.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.346][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-02-06 19:04:18.347][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-02-06 19:04:18.348][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-02-06 19:04:18.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.354][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-02-06 19:04:18.355][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-02-06 19:04:18.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.360][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-02-06 19:04:18.362][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-02-06 19:04:18.363][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-02-06 19:04:18.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.369][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:04:18.370][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-02-06 19:04:18.371][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-02-06 19:04:18.373][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-02-06 19:04:18.374][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-02-06 19:04:18.376][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-02-06 19:04:18.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.381][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-02-06 19:04:18.383][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-02-06 19:04:18.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.388][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-02-06 19:04:18.389][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-02-06 19:04:18.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.395][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-02-06 19:04:18.396][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-02-06 19:04:18.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.401][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-02-06 19:04:18.403][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-02-06 19:04:18.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.408][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-02-06 19:04:18.410][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-02-06 19:04:18.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.415][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-02-06 19:04:18.417][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-02-06 19:04:18.421][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-02-06 19:04:18.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.426][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-02-06 19:04:18.428][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-02-06 19:04:18.429][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-02-06 19:04:18.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.435][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-02-06 19:04:18.437][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:18.439][self$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[2023-02-06 19:04:18.440][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.442][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:04:18.443][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.444][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:04:18.446][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:18.447][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:04:18.449][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:04:18.450][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:04:18.452][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.453][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-02-06 19:04:18.454][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:04:18.456][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.457][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.459][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:04:18.459][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:04:18.459][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:04:18.459][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:04:18.459][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:04:18.460][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:04:18.461][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:18.463][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:18.464][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:04:18.465][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:18.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:18.468][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:04:18.470][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.471][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:04:18.472][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:04:18.473][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:18.475][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.477][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-02-06 19:04:18.479][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:18.481][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:04:18.482][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.483][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:04:18.485][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.486][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:04:18.488][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:18.489][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:04:18.490][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:04:18.492][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:04:18.493][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.495][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-02-06 19:04:18.496][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:04:18.498][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.499][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.501][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:04:18.501][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:04:18.501][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-02-06 19:04:18.501][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-02-06 19:04:18.501][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-02-06 19:04:18.502][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:04:18.504][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:18.505][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:18.506][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:04:18.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:18.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:18.511][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:04:18.512][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.514][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:04:18.515][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:04:18.516][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:18.518][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.520][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-02-06 19:04:18.522][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.524][self$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[2023-02-06 19:04:18.525][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.526][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:04:18.528][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.529][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:04:18.531][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:18.532][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:04:18.534][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:04:18.535][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:04:18.536][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:18.538][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-02-06 19:04:18.539][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:04:18.541][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.542][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.543][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.545][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:04:18.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:18.547][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:18.549][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:04:18.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:18.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:18.553][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:04:18.554][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.555][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:04:18.557][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:04:18.558][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:18.559][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.588][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-02-06 19:04:18.591][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.593][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-02-06 19:04:18.594][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.595][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:04:18.597][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.598][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:04:18.600][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:18.601][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:04:18.602][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-02-06 19:04:18.604][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:04:18.605][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:18.607][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-02-06 19:04:18.608][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:04:18.610][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.611][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:18.612][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.614][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:04:18.615][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:18.616][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:18.618][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:04:18.619][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:18.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:18.622][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:04:18.623][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.625][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:04:18.626][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:04:18.627][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:18.629][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:18.630][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:04:18.632][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.633][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[2023-02-06 19:04:18.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.658][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[2023-02-06 19:04:18.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.743][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-02-06 19:04:18.745][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-02-06 19:04:18.747][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-02-06 19:04:18.749][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-02-06 19:04:18.751][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-02-06 19:04:18.753][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-02-06 19:04:18.755][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-02-06 19:04:18.757][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-02-06 19:04:18.759][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-02-06 19:04:18.762][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-02-06 19:04:18.764][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-02-06 19:04:18.766][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-02-06 19:04:18.768][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-02-06 19:04:18.770][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-02-06 19:04:18.772][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-02-06 19:04:18.774][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:04:18.776][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-02-06 19:04:18.778][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-02-06 19:04:18.780][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-02-06 19:04:18.782][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-02-06 19:04:18.784][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-02-06 19:04:18.786][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-02-06 19:04:18.789][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-02-06 19:04:18.791][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-02-06 19:04:18.793][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-02-06 19:04:18.795][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-02-06 19:04:18.797][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-02-06 19:04:18.799][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-02-06 19:04:18.801][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-02-06 19:04:18.803][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-02-06 19:04:18.805][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-02-06 19:04:18.808][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-02-06 19:04:18.810][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-02-06 19:04:18.812][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-02-06 19:04:18.814][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-02-06 19:04:18.816][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-02-06 19:04:18.818][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-02-06 19:04:18.820][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-02-06 19:04:18.822][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-02-06 19:04:18.824][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-02-06 19:04:18.826][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-02-06 19:04:18.828][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-02-06 19:04:18.830][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-02-06 19:04:18.832][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-02-06 19:04:18.834][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-02-06 19:04:18.836][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-02-06 19:04:18.838][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-02-06 19:04:18.840][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-02-06 19:04:18.842][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-02-06 19:04:18.844][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-02-06 19:04:18.846][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-02-06 19:04:18.848][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-02-06 19:04:18.850][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-02-06 19:04:18.852][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-02-06 19:04:18.854][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-02-06 19:04:18.856][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-02-06 19:04:18.858][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-02-06 19:04:18.861][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-02-06 19:04:18.863][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-02-06 19:04:18.865][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-02-06 19:04:18.867][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-02-06 19:04:18.869][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-02-06 19:04:18.871][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-02-06 19:04:18.873][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-02-06 19:04:18.875][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-02-06 19:04:18.877][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-02-06 19:04:18.879][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-02-06 19:04:18.881][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-02-06 19:04:18.883][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-02-06 19:04:18.885][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-02-06 19:04:18.887][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-02-06 19:04:18.889][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-02-06 19:04:18.891][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-02-06 19:04:18.893][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-02-06 19:04:18.895][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-02-06 19:04:18.897][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-02-06 19:04:18.899][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-02-06 19:04:18.902][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-02-06 19:04:18.904][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-02-06 19:04:18.906][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-02-06 19:04:18.908][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-02-06 19:04:18.910][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-02-06 19:04:18.912][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-02-06 19:04:18.914][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-02-06 19:04:18.916][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-02-06 19:04:18.918][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-02-06 19:04:18.919][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.921][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.923][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[2023-02-06 19:04:18.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:18.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:18.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:18.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:18.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:18.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:18.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:18.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:18.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:18.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:18.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:18.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:18.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:18.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:18.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:18.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:18.996][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[2023-02-06 19:04:18.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:18.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:18.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:19.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:19.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:19.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:19.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:19.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:19.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:19.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:19.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:19.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:19.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:19.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:19.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:19.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:19.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:19.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:19.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:19.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:19.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:19.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:19.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:19.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:19.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:19.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:19.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:19.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:19.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:19.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:19.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:19.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:19.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:19.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:19.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:19.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:19.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:19.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:19.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:19.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:19.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:19.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:19.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:19.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:19.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:19.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:19.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:19.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:19.056][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[2023-02-06 19:04:19.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:19.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:19.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:19.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:19.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:19.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:19.065][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[2023-02-06 19:04:19.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:19.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:19.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:19.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:19.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:19.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:19.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:19.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:19.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:19.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:19.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:19.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:19.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:19.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:19.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-02-06 19:04:19.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:19.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:19.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:19.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:19.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:19.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-02-06 19:04:19.093][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-02-06 19:04:19.095][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-02-06 19:04:19.097][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:19.098][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-02-06 19:04:19.100][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:19.101][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-02-06 19:04:19.103][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:19.104][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-02-06 19:04:19.105][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:19.107][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-02-06 19:04:19.108][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-02-06 19:04:19.109][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-02-06 19:04:19.111][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:19.112][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-02-06 19:04:19.113][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-02-06 19:04:19.115][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-02-06 19:04:19.115][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-02-06 19:04:19.115][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-02-06 19:04:19.115][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-02-06 19:04:19.115][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-02-06 19:04:19.115][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-02-06 19:04:19.115][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-02-06 19:04:19.115][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-02-06 19:04:19.115][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-02-06 19:04:19.116][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-02-06 19:04:19.118][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-02-06 19:04:19.118][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-02-06 19:04:19.119][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-02-06 19:04:19.120][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:19.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:19.123][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-02-06 19:04:19.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-02-06 19:04:19.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-02-06 19:04:19.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-02-06 19:04:19.128][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-02-06 19:04:19.128][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-02-06 19:04:19.130][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-02-06 19:04:19.131][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-02-06 19:04:19.132][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-02-06 19:04:19.134][self$setPropertyValue]
biodb.DEBUG[2023-02-06 19:04:19.135][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-02-06 19:04:19.138][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-02-06 19:04:19.142][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-02-06 19:04:19.144][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-02-06 19:04:19.145][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-02-06 19:04:19.147][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-02-06 19:04:19.149][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-02-06 19:04:19.150][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-02-06 19:04:19.152][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-02-06 19:04:19.153][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-02-06 19:04:19.155][biodb::testThat]
biodb.INFO [2023-02-06 19:04:19.157][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2023-02-06 19:04:19.158][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-02-06 19:04:19.159][biodb::testThat]
biodb.DEBUG[2023-02-06 19:04:19.165][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-02-06 19:04:19.170][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-02-06 19:04:19.172][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-02-06 19:04:19.174][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-02-06 19:04:19.261][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-02-06 19:04:20.369][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-02-06 19:04:20.371][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-02-06 19:04:20.373][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-02-06 19:04:20.375][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-02-06 19:04:20.377][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2023-02-06 19:04:20.379][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-02-06 19:04:20.399][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-02-06 19:04:20.400][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-02-06 19:04:20.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:04:20.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:20.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:20.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:20.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:20.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:20.417][FUN] Functions in observer BiodbConfig: [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[2023-02-06 19:04:20.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:20.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:20.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:20.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:20.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.456][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:04:20.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:04:20.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.463][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:04:20.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:04:20.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.469][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:20.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:20.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.475][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:20.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:20.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.485][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:20.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:20.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.492][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:20.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:20.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.502][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:04:20.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:20.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.508][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:04:20.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:20.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:20.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:20.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:20.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:20.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.536][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.552][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:04:20.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.558][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-06 19:04:20.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.570][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.576][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:04:20.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.655][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.664][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:20.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:20.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.670][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:20.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:20.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.681][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:20.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:20.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:04:20.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:04:20.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:20.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:20.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:20.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:20.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:20.725][FUN] Functions in observer BiodbConfig: [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[2023-02-06 19:04:20.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:20.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:20.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:20.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:20.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.785][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:04:20.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-02-06 19:04:20.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.791][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:04:20.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-02-06 19:04:20.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.796][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:20.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:20.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.802][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:20.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:20.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.811][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:20.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:20.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.817][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:20.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:20.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.826][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:04:20.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:20.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.832][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-02-06 19:04:20.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:20.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.841][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:20.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:20.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.849][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:20.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:20.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.858][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.864][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.874][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:04:20.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.880][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-02-06 19:04:20.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.886][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:20.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.897][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-02-06 19:04:20.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:20.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.907][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:20.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:20.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.912][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:20.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:20.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.923][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:20.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:20.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:20.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:20.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:20.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:20.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-02-06 19:04:20.985][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-02-06 19:04:20.988][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-02-06 19:04:20.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:04:20.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:20.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:21.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:21.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:21.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:21.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:04:21.007][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:04:21.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:04:21.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.013][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:04:21.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:04:21.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.019][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-06 19:04:21.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-06 19:04:21.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.025][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-06 19:04:21.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-06 19:04:21.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.030][private$selectFields] Fields none
biodb.TRACE[2023-02-06 19:04:21.032][private$selectFields]
biodb.TRACE[2023-02-06 19:04:21.033][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-02-06 19:04:21.034][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:04:21.036][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:04:21.037][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:21.039][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:21.040][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.042][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.043][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.044][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.046][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.047][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.049][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.050][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.053][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.054][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.056][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.057][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.058][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.060][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.061][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.063][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.064][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.065][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:21.067][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:21.068][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.070][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.071][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:21.073][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:21.074][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.075][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.077][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.078][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.080][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.081][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.082][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:21.084][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:21.085][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.086][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.088][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.089][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.091][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.092][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.093][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.095][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.096][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.098][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.099][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.100][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.102][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.103][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.105][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.106][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.107][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.109][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.110][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:21.112][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:21.113][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.114][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.116][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:21.117][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:21.118][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.120][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.121][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.123][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.124][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.125][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.127][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:04:21.128][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:04:21.130][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:21.131][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:21.132][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.134][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.135][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.137][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.138][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.139][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.141][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.142][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.144][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.145][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.146][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.148][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.149][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.151][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.171][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.172][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.174][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.175][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.176][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:21.178][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:21.179][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.180][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.182][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:21.183][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:21.184][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.186][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.187][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.188][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.190][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.191][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.192][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-02-06 19:04:21.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:21.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:21.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:21.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:21.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:21.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:21.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.227][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.233][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.238][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.244][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.250][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.256][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.279][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:21.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:21.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.285][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:21.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:21.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.291][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:21.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:21.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:21.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:21.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:21.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:21.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:21.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:21.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.314][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.320][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.325][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.339][private$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[2023-02-06 19:04:21.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-02-06 19:04:21.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:21.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:21.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:21.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:21.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:21.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-02-06 19:04:21.357][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:04:21.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:04:21.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.362][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-02-06 19:04:21.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-02-06 19:04:21.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.368][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-02-06 19:04:21.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-02-06 19:04:21.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.374][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-02-06 19:04:21.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-02-06 19:04:21.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.379][private$selectFields] Fields none
biodb.TRACE[2023-02-06 19:04:21.380][private$selectFields]
biodb.TRACE[2023-02-06 19:04:21.382][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-02-06 19:04:21.383][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-02-06 19:04:21.384][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:04:21.386][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:21.387][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:21.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.390][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.391][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.393][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.396][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.397][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.398][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.400][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.401][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.402][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.404][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.405][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.407][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.408][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.409][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.411][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.412][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.413][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:21.415][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:21.416][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.418][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.419][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:21.421][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:21.422][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.423][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.425][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.426][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.427][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.429][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.430][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:21.432][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:21.433][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.434][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.436][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.437][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.438][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.440][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.441][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.443][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.444][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.445][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.447][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.448][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.450][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.451][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.452][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.454][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.455][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.456][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.458][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:21.459][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:21.461][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.462][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.463][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:21.465][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:21.466][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.468][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.469][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.470][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.472][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.473][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.474][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:04:21.476][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-02-06 19:04:21.477][ef$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:21.479][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:21.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.481][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.483][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.484][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.485][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.487][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.488][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.490][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.491][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.492][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.494][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.495][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.497][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.498][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.499][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.501][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.502][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.503][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.505][ef$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:21.506][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:21.508][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.509][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.510][ef$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:21.512][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:21.513][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.515][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.516][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.518][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.519][ef$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.520][ef$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.522][private$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[2023-02-06 19:04:21.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:21.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:21.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:21.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:21.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-02-06 19:04:21.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-02-06 19:04:21.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-02-06 19:04:21.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.576][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.582][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.587][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-02-06 19:04:21.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.593][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.599][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.604][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-02-06 19:04:21.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-02-06 19:04:21.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.626][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:21.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:21.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.632][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:21.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:21.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.638][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-02-06 19:04:21.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-02-06 19:04:21.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:21.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:21.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:21.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:21.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.655][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-02-06 19:04:21.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-02-06 19:04:21.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.660][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.666][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.671][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-02-06 19:04:21.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-02-06 19:04:21.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-02-06 19:04:21.682][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2023-02-06 19:04:21.684][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-02-06 19:04:21.685][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-02-06 19:04:21.689][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-02-06 19:04:21.690][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-02-06 19:04:21.692][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-02-06 19:04:21.693][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-02-06 19:04:21.694][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-02-06 19:04:21.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-02-06 19:04:21.697][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-02-06 19:04:21.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-02-06 19:04:21.699][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-02-06 19:04:21.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 168 ]
> 
> proc.time()
   user  system elapsed 
 31.220   1.498 147.515

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.8020.2045.625
LipidmapsStructureEntry0.4940.0010.496