Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:10 -0400 (Wed, 19 Oct 2022).

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

CHECK results for biodbLipidmaps on palomino3


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

raw results

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

Summary

Package: biodbLipidmaps
Version: 1.2.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.2.0.tar.gz
StartedAt: 2022-10-18 22:23:32 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:26:38 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 185.3 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

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


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/biodbLipidmaps.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'biodbLipidmaps/DESCRIPTION' ... OK
* this is package 'biodbLipidmaps' version '1.2.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'biodbLipidmaps' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


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

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2022-10-18 22:24:44.386][biodb::testContext]
biodb.INFO [2022-10-18 22:24:44.390][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 22:24:44.392][biodb::testContext] Test context - Generic tests
biodb.INFO [2022-10-18 22:24:44.394][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 22:24:44.396][biodb::testContext]
biodb.INFO [2022-10-18 22:24:44.424][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 22:24:44.428][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 22:24:44.439][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 22:24:44.440][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 22:24:44.442][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 22:24:44.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.447][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 22:24:44.468][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 22:24:44.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.473][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 22:24:44.475][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 22:24:44.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.480][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 22:24:44.481][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 22:24:44.483][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 22:24:44.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.488][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 22:24:44.490][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 22:24:44.491][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 22:24:44.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.498][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 22:24:44.500][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 22:24:44.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.508][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 22:24:44.509][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 22:24:44.511][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 22:24:44.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.528][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 22:24:44.529][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 22:24:44.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.533][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 22:24:44.534][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 22:24:44.536][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 22:24:44.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.540][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 22:24:44.541][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 22:24:44.543][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 22:24:44.544][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 22:24:44.545][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 22:24:44.546][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 22:24:44.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.553][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 22:24:44.554][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 22:24:44.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.560][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 22:24:44.561][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 22:24:44.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.567][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 22:24:44.569][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 22:24:44.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.574][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 22:24:44.576][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 22:24:44.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.581][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 22:24:44.582][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 22:24:44.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.587][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 22:24:44.588][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 22:24:44.591][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 22:24:44.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.596][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 22:24:44.597][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 22:24:44.598][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 22:24:44.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.605][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 22:24:44.639][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:44.653][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 22:24:44.654][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.656][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:24:44.657][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.658][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:24:44.659][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:44.660][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:24:44.662][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 22:24:44.663][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:24:44.664][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.665][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 22:24:44.666][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:24:44.668][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.669][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.670][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 22:24:44.670][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 22:24:44.670][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 22:24:44.670][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 22:24:44.670][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 22:24:44.671][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:24:44.673][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:24:44.674][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:24:44.675][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:24:44.676][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:24:44.677][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:24:44.678][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:24:44.679][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.681][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:24:44.682][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:24:44.683][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:44.684][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.686][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 22:24:44.687][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:44.689][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 22:24:44.690][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.691][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:24:44.692][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.693][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:24:44.695][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:44.696][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:24:44.697][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 22:24:44.698][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:24:44.700][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.701][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 22:24:44.702][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:24:44.703][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.704][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.705][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 22:24:44.705][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 22:24:44.705][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 22:24:44.705][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 22:24:44.705][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 22:24:44.707][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:24:44.708][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:24:44.709][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:24:44.710][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:24:44.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:24:44.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:24:44.714][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:24:44.715][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.716][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:24:44.718][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:24:44.719][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:44.720][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.722][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 22:24:44.724][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.725][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 22:24:44.726][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.727][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:24:44.728][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.730][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:24:44.731][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:44.732][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:24:44.733][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 22:24:44.734][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:24:44.736][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:44.737][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 22:24:44.738][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:24:44.739][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.740][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.742][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.743][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:24:44.744][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:24:44.745][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:24:44.747][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:24:44.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:24:44.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:24:44.751][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:24:44.752][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.753][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:24:44.755][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:24:44.757][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:44.758][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.765][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 22:24:44.767][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.768][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 22:24:44.770][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.771][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:24:44.772][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.773][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:24:44.774][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:44.775][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:24:44.777][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 22:24:44.778][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:24:44.779][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:44.780][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 22:24:44.781][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:24:44.783][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.784][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:44.785][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.786][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:24:44.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:24:44.788][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:24:44.790][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:24:44.791][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:24:44.792][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:24:44.793][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:24:44.794][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.795][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:24:44.796][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:24:44.798][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:44.799][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:44.803][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 22:24:44.804][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.810][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[2022-10-18 22:24:44.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.827][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[2022-10-18 22:24:44.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.860][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[2022-10-18 22:24:44.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:44.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:44.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:44.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:44.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:44.900][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 22:24:44.905][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 22:24:44.906][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 22:24:44.908][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 22:24:44.910][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 22:24:44.911][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 22:24:44.913][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 22:24:44.915][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 22:24:44.916][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 22:24:44.918][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 22:24:44.920][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 22:24:44.921][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 22:24:44.923][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 22:24:44.924][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 22:24:44.926][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 22:24:44.928][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 22:24:44.929][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 22:24:44.931][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 22:24:44.932][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 22:24:44.934][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 22:24:44.936][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 22:24:44.937][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 22:24:44.939][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 22:24:44.940][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 22:24:44.942][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 22:24:44.943][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 22:24:44.945][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 22:24:44.947][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 22:24:44.948][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 22:24:44.950][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 22:24:44.951][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 22:24:44.953][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 22:24:44.954][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 22:24:44.956][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 22:24:44.958][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 22:24:44.959][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 22:24:44.961][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 22:24:44.962][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 22:24:44.964][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 22:24:44.965][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 22:24:44.967][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 22:24:44.969][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 22:24:44.970][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 22:24:44.972][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 22:24:44.973][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 22:24:44.975][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 22:24:44.977][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 22:24:44.978][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 22:24:44.980][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 22:24:44.981][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 22:24:44.983][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 22:24:44.984][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 22:24:44.986][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 22:24:44.988][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 22:24:44.989][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 22:24:44.991][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 22:24:44.993][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 22:24:45.000][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 22:24:45.002][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 22:24:45.004][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 22:24:45.005][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 22:24:45.007][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 22:24:45.008][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 22:24:45.010][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 22:24:45.012][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 22:24:45.013][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 22:24:45.015][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 22:24:45.016][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 22:24:45.018][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 22:24:45.019][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 22:24:45.021][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 22:24:45.023][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 22:24:45.024][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 22:24:45.026][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 22:24:45.027][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 22:24:45.029][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 22:24:45.031][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 22:24:45.032][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 22:24:45.034][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 22:24:45.035][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 22:24:45.037][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 22:24:45.039][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 22:24:45.040][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 22:24:45.070][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 22:24:45.073][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 22:24:45.076][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 22:24:45.077][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.080][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.096][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.DEBUG[2022-10-18 22:24:45.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.149][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[2022-10-18 22:24:45.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.194][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[2022-10-18 22:24:45.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:24:45.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:24:45.219][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.15-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-10-18 22:24:45.228][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 22:24:45.231][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:45.233][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 22:24:45.234][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:45.235][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:24:45.237][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:45.239][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:24:45.240][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:45.241][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:24:45.242][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 22:24:45.244][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:24:45.245][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:45.247][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-10-18 22:24:45.248][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:24:45.249][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-10-18 22:24:45.249][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-10-18 22:24:45.249][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-10-18 22:24:45.249][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-10-18 22:24:45.249][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-10-18 22:24:45.249][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-10-18 22:24:45.249][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-10-18 22:24:45.249][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-10-18 22:24:45.249][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-10-18 22:24:45.250][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 22:24:45.257][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 22:24:45.257][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 22:24:45.258][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:24:45.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:24:45.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:24:45.261][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:24:45.263][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:24:45.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:24:45.265][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:24:45.266][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 22:24:45.266][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-10-18 22:24:45.267][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:24:45.268][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:24:45.270][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 22:24:45.271][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:24:45.276][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-10-18 22:24:45.278][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 22:24:45.302][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 22:24:45.303][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-10-18 22:24:45.307][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 22:24:45.312][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-10-18 22:24:45.316][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 22:24:45.317][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 22:24:45.319][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-10-18 22:24:45.320][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-10-18 22:24:45.339][biodb::testThat]
biodb.INFO [2022-10-18 22:24:45.340][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2022-10-18 22:24:45.342][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:24:45.343][biodb::testThat]
biodb.TRACE[2022-10-18 22:24:45.348][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.15-bioc/R/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2022-10-18 22:24:45.355][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-10-18 22:24:45.360][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 22:24:45.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:24:45.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:45.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:45.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:45.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:45.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:45.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:24:45.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:24:45.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:24:45.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.439][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:24:45.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:24:45.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.444][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:24:45.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:24:45.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.450][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:45.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:45.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.487][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:45.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:45.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.501][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:45.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:45.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.547][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:45.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:45.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.556][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:24:45.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:45.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.562][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:24:45.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:45.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.571][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:24:45.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:24:45.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.576][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:24:45.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:24:45.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.601][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:24:45.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.606][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 22:24:45.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.625][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:24:45.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.652][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.657][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.703][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.711][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.716][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.734][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:24:45.775][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2022-10-18 22:24:45.784][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 22:24:45.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 22:24:45.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.789][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 22:24:45.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 22:24:45.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.795][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 22:24:45.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 22:24:45.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.800][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 22:24:45.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 22:24:45.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.846][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.890][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.897][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.903][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:45.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.932][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.934][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.935][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.936][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:45.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:45.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.973][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.974][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.975][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.976][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:45.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:45.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.992][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:45.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:45.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:45.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:45.999][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.005][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.013][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.015][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.016][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.017][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.019][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:24:46.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:24:46.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.037][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:24:46.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:24:46.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.042][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:24:46.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:24:46.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.047][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:24:46.049][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:24:46.050][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.051][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.052][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:24:46.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:24:46.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.081][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.082][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.083][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.084][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.099][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.104][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.109][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.114][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.115][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.117][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.118][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.120][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.136][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:46.137][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:46.139][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.140][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.147][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.149][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.150][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.151][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.159][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:24:46.160][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:24:46.161][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.162][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.169][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.171][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.177][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.178][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.185][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.187][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.188][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.189][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.196][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.198][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.199][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.200][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 22:24:46.209][biodb::testThat]
biodb.INFO [2022-10-18 22:24:46.210][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-10-18 22:24:46.211][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:24:46.212][biodb::testThat]
biodb.DEBUG[2022-10-18 22:24:46.226][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2022-10-18 22:24:46.233][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 22:24:46.241][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2022-10-18 22:24:46.243][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 22:24:46.245][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2022-10-18 22:24:46.246][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 22:24:46.286][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-10-18 22:24:46.288][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 22:24:46.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:24:46.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:24:46.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:24:46.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:24:46.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:24:46.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:24:46.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:24:46.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:46.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:46.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:46.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:46.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:24:46.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:24:46.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:24:46.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:24:46.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.349][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:24:46.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:24:46.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.354][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:24:46.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:24:46.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.359][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.364][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:24:46.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.381][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.386][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:24:46.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.395][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:24:46.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.400][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:24:46.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:46.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.409][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:24:46.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:24:46.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:24:46.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:24:46.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.428][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.436][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:24:46.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.441][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 22:24:46.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.446][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.452][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.460][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:24:46.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.478][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.501][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:46.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:46.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.506][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:46.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:46.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:46.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:46.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.515][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:46.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:24:46.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:46.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:46.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:46.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:46.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:46.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:46.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:46.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:46.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:46.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:46.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:24:46.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:24:46.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:24:46.560][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2022-10-18 22:24:46.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-10-18 22:24:46.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-10-18 22:24:46.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-10-18 22:24:46.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-10-18 22:24:46.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-10-18 22:24:46.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-10-18 22:24:46.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 22:24:46.587][biodb::testThat]
biodb.INFO [2022-10-18 22:24:46.594][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2022-10-18 22:24:46.596][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:24:46.597][biodb::testThat]
biodb.TRACE[2022-10-18 22:24:46.600][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.601][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.602][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.604][ef$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:24:46.605][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2022-10-18 22:24:46.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:46.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:46.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:46.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:46.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:24:46.672][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 22:24:46.872][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 22:24:46.896][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:24:46.898][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:24:46.901][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2022-10-18 22:24:47.597][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride does not exist.
biodb.TRACE[2022-10-18 22:24:47.599][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:24:47.603][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:24:47.606][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2022-10-18 22:24:48.255][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:24:48.265][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2022-10-18 22:24:48.291][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2022-10-18 22:24:48.297][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2022-10-18 22:24:48.324][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:48.325][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:48.326][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:48.328][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 22:24:48.330][biodb::testThat]
biodb.INFO [2022-10-18 22:24:48.332][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2022-10-18 22:24:48.333][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:24:48.334][biodb::testThat]
biodb.TRACE[2022-10-18 22:24:48.376][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:48.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:48.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:48.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:48.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:48.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:48.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:48.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:48.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:48.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:48.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:48.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:24:48.552][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 22:24:48.555][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 22:24:48.570][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-10-18 22:24:48.572][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 22:24:48.574][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2022-10-18 22:24:48.602][biodb::testThat]
biodb.INFO [2022-10-18 22:24:48.604][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2022-10-18 22:24:48.605][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:24:48.606][biodb::testThat]
biodb.TRACE[2022-10-18 22:24:48.636][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 22:24:48.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 22:24:48.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:48.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:48.641][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 22:24:48.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 22:24:48.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:48.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:48.646][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 22:24:48.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 22:24:48.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:48.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:48.651][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 22:24:48.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 22:24:48.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:48.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:48.695][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 22:24:48.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 22:24:48.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:48.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:48.706][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 22:24:48.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 22:24:48.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:48.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:48.710][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 22:24:48.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 22:24:48.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:48.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:48.716][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 22:24:48.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 22:24:48.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:48.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 22:24:48.724][biodb::testThat]
biodb.INFO [2022-10-18 22:24:48.725][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-10-18 22:24:48.727][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:24:48.728][biodb::testThat]
biodb.INFO [2022-10-18 22:24:48.734][biodb::testThat]
biodb.INFO [2022-10-18 22:24:48.736][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-10-18 22:24:48.737][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:24:48.738][biodb::testThat]
biodb.INFO [2022-10-18 22:24:48.744][biodb::testThat]
biodb.INFO [2022-10-18 22:24:48.746][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2022-10-18 22:24:48.747][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:24:48.748][biodb::testThat]
biodb.DEBUG[2022-10-18 22:24:48.753][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2022-10-18 22:24:49.066][getUrlContent] Use base::url() for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2022-10-18 22:24:49.826][biodb::testThat]
biodb.INFO [2022-10-18 22:24:49.828][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2022-10-18 22:24:49.829][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:24:49.830][biodb::testThat]
biodb.TRACE[2022-10-18 22:24:49.843][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:49.845][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:49.847][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:49.848][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:49.849][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:49.851][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:49.852][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:49.853][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 22:24:49.856][biodb::testThat]
biodb.INFO [2022-10-18 22:24:49.857][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2022-10-18 22:24:49.859][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:24:49.860][biodb::testThat]
biodb.TRACE[2022-10-18 22:24:49.885][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:49.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:49.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:49.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:49.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:49.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:49.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:49.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:49.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:24:49.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:24:49.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:49.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:24:50.147][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 22:24:50.151][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 22:24:50.153][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-10-18 22:24:50.155][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 22:24:50.157][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2022-10-18 22:24:50.338][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2022-10-18 22:24:50.342][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 22:24:50.344][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2022-10-18 22:24:50.346][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 22:24:50.348][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2022-10-18 22:24:50.370][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 22:24:50.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 22:24:50.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:50.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:50.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 22:24:50.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 22:24:50.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:50.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:50.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:50.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:50.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:50.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:50.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:50.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:50.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:50.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:50.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:50.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:50.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:50.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:50.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:50.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:50.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:50.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:24:50.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:50.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:24:50.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:24:50.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:24:50.513][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2022-10-18 22:24:50.530][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:24:50.531][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:24:50.547][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2022-10-18 22:24:50.867][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2022-10-18 22:24:50.868][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:24:50.870][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:24:50.872][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2022-10-18 22:24:56.931][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:24:56.941][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2022-10-18 22:24:57.048][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2022-10-18 22:25:00.358][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2022-10-18 22:25:00.364][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:00.366][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:25:00.370][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2022-10-18 22:25:00.701][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06 does not exist.
biodb.TRACE[2022-10-18 22:25:00.704][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:00.707][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:00.711][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2022-10-18 22:25:01.315][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:25:01.325][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2022-10-18 22:25:01.341][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2022-10-18 22:25:01.455][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2022-10-18 22:25:01.460][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:01.462][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:25:01.465][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2022-10-18 22:25:01.785][doesRCurlRequestUrlExist] According to RCurl, URL 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 does not exist.
biodb.TRACE[2022-10-18 22:25:01.787][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:01.789][getUrlRequestResult] URL "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" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:01.792][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2022-10-18 22:25:02.406][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:25:02.423][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2022-10-18 22:25:02.449][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2022-10-18 22:25:02.505][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 22:25:02.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 22:25:02.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:02.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 22:25:02.541][biodb::testThat]
biodb.INFO [2022-10-18 22:25:02.544][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2022-10-18 22:25:02.546][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:25:02.548][biodb::testThat]
biodb.TRACE[2022-10-18 22:25:02.555][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 22:25:02.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 22:25:02.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:02.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:02.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 22:25:02.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 22:25:02.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:02.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:02.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:02.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:02.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:02.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:02.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:02.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:02.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:02.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:02.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:02.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:02.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:02.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:02.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:02.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:02.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:02.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:25:02.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:02.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:02.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:02.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:02.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:02.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:02.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:25:02.863][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2022-10-18 22:25:02.869][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:02.871][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:25:02.875][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2022-10-18 22:25:03.205][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01 does not exist.
biodb.TRACE[2022-10-18 22:25:03.207][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:03.211][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:03.213][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2022-10-18 22:25:10.138][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:25:10.149][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2022-10-18 22:25:10.272][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2022-10-18 22:25:13.559][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2022-10-18 22:25:13.614][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-10-18 22:25:13.616][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2022-10-18 22:25:13.618][cch$loadFileContent] file.exist = [2]: "TRUE, FALSE".
biodb.TRACE[2022-10-18 22:25:13.627][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2022-10-18 22:25:13.631][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 22:25:13.634][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 22:25:13.637][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 22:25:13.639][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 22:25:13.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:13.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:13.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:13.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:13.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:13.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:13.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:25:13.657][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2022-10-18 22:25:13.660][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:13.661][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:25:13.663][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2022-10-18 22:25:13.977][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:13.978][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:13.980][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:13.981][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2022-10-18 22:25:14.646][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:25:14.655][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2022-10-18 22:25:14.669][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2022-10-18 22:25:14.684][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2022-10-18 22:25:14.693][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 22:25:14.721][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-10-18 22:25:14.724][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 22:25:14.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:14.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:14.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:14.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:14.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:14.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:14.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:14.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:14.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:14.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:14.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:14.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:25:14.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:25:14.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:25:14.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:25:14.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.799][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:25:14.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:25:14.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.807][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:25:14.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:25:14.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.813][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:25:14.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:25:14.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.820][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:25:14.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:25:14.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.829][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:25:14.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:25:14.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.835][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:25:14.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:25:14.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.845][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:25:14.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:14.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:25:14.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:14.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.859][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:25:14.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:25:14.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.864][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:25:14.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:25:14.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:14.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:14.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:14.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:14.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.887][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:25:14.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:14.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.892][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 22:25:14.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:14.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.896][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:14.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:14.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:14.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:14.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.906][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:25:14.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:14.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.915][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:14.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:14.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.921][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:14.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:14.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:14.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:14.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.931][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:14.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:14.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:14.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:14.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:14.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:14.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:14.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:14.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:25:14.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:14.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:14.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:14.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:14.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:14.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:14.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:14.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:14.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:14.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:14.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:14.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:25:14.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:25:14.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:14.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:14.997][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:25:14.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:25:15.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.002][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:25:15.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:25:15.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.020][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:25:15.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:25:15.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.026][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:25:15.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:25:15.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.035][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:25:15.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:25:15.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.042][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:25:15.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:25:15.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.055][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:25:15.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:15.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.061][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:25:15.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:15.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:25:15.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:25:15.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:25:15.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:25:15.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:15.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:15.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:15.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:15.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.102][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:25:15.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:15.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.108][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 22:25:15.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:15.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.115][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:15.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:15.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:15.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:15.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.126][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:25:15.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:15.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.137][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.142][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:15.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:15.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.152][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:15.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:15.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:15.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:15.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:15.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:15.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:15.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:15.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:15.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:15.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:15.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:15.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:15.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:15.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:15.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:15.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:15.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:15.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:25:15.212][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2022-10-18 22:25:15.221][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 22:25:15.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:15.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:15.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:15.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:15.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:15.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:15.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:15.240][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.246][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.251][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:15.252][private$selectFields]
biodb.TRACE[2022-10-18 22:25:15.254][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 22:25:15.255][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 22:25:15.256][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:15.257][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.259][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.260][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.261][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.262][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.264][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.265][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.266][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.267][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:15.268][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:15.270][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.271][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.272][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.273][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.275][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 22:25:15.276][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.281][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.286][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.299][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-10-18 22:25:15.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:15.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:15.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:15.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:15.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:15.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:15.315][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.TRACE[2022-10-18 22:25:15.316][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.321][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.326][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:15.328][private$selectFields]
biodb.TRACE[2022-10-18 22:25:15.329][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 22:25:15.330][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 22:25:15.331][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:15.332][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.334][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.335][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.336][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.337][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.339][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.340][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.341][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.342][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:15.344][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:15.345][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.346][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.348][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.349][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.350][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 22:25:15.351][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.356][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.361][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.367][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-10-18 22:25:15.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:15.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:15.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:15.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:15.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:15.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:15.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:15.383][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.389][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.393][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:15.395][private$selectFields]
biodb.TRACE[2022-10-18 22:25:15.396][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 22:25:15.397][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 22:25:15.398][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:15.400][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.401][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.402][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.403][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.405][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.406][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.407][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.409][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.410][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:15.411][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:15.412][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.413][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.415][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.416][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.417][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 22:25:15.419][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.423][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.429][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:15.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.447][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-10-18 22:25:15.449][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 22:25:15.451][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 22:25:15.464][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 22:25:15.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 22:25:15.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 22:25:15.475][biodb::testThat]
biodb.INFO [2022-10-18 22:25:15.477][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2022-10-18 22:25:15.479][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:25:15.481][biodb::testThat]
biodb.TRACE[2022-10-18 22:25:15.486][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 22:25:15.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 22:25:15.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 22:25:15.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 22:25:15.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:15.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:15.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:15.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:15.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:15.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:15.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:15.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:15.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:15.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:15.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:25:15.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:15.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:15.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:15.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:15.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:15.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:15.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:25:15.733][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2022-10-18 22:25:15.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:15.741][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:25:15.745][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2022-10-18 22:25:16.062][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375 does not exist.
biodb.TRACE[2022-10-18 22:25:16.063][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:16.065][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:16.067][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2022-10-18 22:25:22.003][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:25:22.014][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2022-10-18 22:25:22.392][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2022-10-18 22:25:25.394][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 22:25:25.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:25.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:25.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:25.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:25.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:25.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:25.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:25.445][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.451][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.476][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:25.478][private$selectFields]
biodb.TRACE[2022-10-18 22:25:25.479][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 22:25:25.480][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 22:25:25.482][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:25.483][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.485][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.486][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.488][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.489][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.490][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.491][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.493][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.494][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:25.504][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:25.506][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.507][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.508][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.509][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.510][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 22:25:25.512][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.517][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.522][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.527][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-10-18 22:25:25.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:25.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:25.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:25.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:25.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:25.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:25.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:25.543][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.549][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.554][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:25.555][private$selectFields]
biodb.TRACE[2022-10-18 22:25:25.556][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 22:25:25.557][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 22:25:25.558][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:25.560][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.561][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.562][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.563][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.565][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.566][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.567][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.569][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.571][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:25.573][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:25.575][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.577][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.579][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.581][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.583][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 22:25:25.585][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.594][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.603][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.612][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-10-18 22:25:25.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:25.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:25.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:25.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:25.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:25.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:25.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:25.632][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.637][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.642][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:25.643][private$selectFields]
biodb.TRACE[2022-10-18 22:25:25.645][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 22:25:25.647][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 22:25:25.648][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:25.649][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.650][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.651][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.653][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.654][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.656][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.658][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.659][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.661][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:25.663][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:25.665][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.667][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.669][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.670][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.672][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 22:25:25.674][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.681][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.687][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:25.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.692][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-10-18 22:25:25.694][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 22:25:25.695][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 22:25:25.705][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 22:25:25.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 22:25:25.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 22:25:25.712][biodb::testThat]
biodb.INFO [2022-10-18 22:25:25.713][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2022-10-18 22:25:25.714][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:25:25.715][biodb::testThat]
biodb.TRACE[2022-10-18 22:25:25.719][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2022-10-18 22:25:25.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2022-10-18 22:25:25.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-18 22:25:25.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-18 22:25:25.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:25.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:25.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:25.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:25.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:25.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:25.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:25.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:25.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:25.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:25.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:25:25.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:25.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:25.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:25.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:25.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:25.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:25.820][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[2022-10-18 22:25:26.015][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.INFO [2022-10-18 22:25:26.020][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.DEBUG[2022-10-18 22:25:26.023][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:26.025][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:25:26.029][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2022-10-18 22:25:26.351][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01 does not exist.
biodb.TRACE[2022-10-18 22:25:26.353][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:26.357][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:26.360][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2022-10-18 22:25:32.605][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:25:32.616][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2022-10-18 22:25:32.724][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2022-10-18 22:25:35.306][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 22:25:35.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:35.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:35.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:35.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:35.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:35.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:35.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:35.327][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.335][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.341][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:35.342][private$selectFields]
biodb.TRACE[2022-10-18 22:25:35.344][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 22:25:35.345][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 22:25:35.346][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:35.348][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.350][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.352][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.353][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.355][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.357][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.359][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.360][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.361][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:35.362][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:35.364][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.365][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.366][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.368][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.370][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 22:25:35.372][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.378][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.384][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.389][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2022-10-18 22:25:35.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:35.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:35.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:35.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:35.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:35.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:35.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:35.405][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.410][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.415][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:35.416][private$selectFields]
biodb.TRACE[2022-10-18 22:25:35.417][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 22:25:35.419][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 22:25:35.420][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:35.422][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.424][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.426][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.427][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.429][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.431][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.432][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.433][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.435][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:35.436][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:35.438][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.440][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.441][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.443][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.445][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 22:25:35.447][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.453][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.460][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.466][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2022-10-18 22:25:35.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:35.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:35.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:35.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:35.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:35.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:35.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:35.488][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.493][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.498][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:35.500][private$selectFields]
biodb.TRACE[2022-10-18 22:25:35.501][private$selectFields] Fields is null: FALSE
biodb.TRACE[2022-10-18 22:25:35.503][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 22:25:35.505][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:35.507][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.509][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.510][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.512][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.513][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.514][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.516][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.517][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.519][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:35.521][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:25:35.523][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.525][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.527][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.528][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.529][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2022-10-18 22:25:35.530][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.537][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.545][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:35.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:35.550][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2022-10-18 22:25:35.552][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 22:25:35.553][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2022-10-18 22:25:35.589][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2022-10-18 22:25:35.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2022-10-18 22:25:35.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:35.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-18 22:25:35.598][biodb::testThat]
biodb.INFO [2022-10-18 22:25:35.600][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2022-10-18 22:25:35.602][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:25:35.603][biodb::testThat]
biodb.DEBUG[2022-10-18 22:25:35.606][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2022-10-18 22:25:35.607][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2022-10-18 22:25:35.609][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2022-10-18 22:25:35.611][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2022-10-18 22:25:35.614][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 22:25:35.616][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 22:25:35.618][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 22:25:35.620][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 22:25:35.621][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 22:25:35.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:35.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:35.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:35.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:35.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:35.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:35.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:25:35.671][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2022-10-18 22:25:35.675][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:35.676][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:25:35.678][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 22:25:36.015][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:36.017][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:36.019][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:36.021][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 22:25:36.635][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:36.637][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:36.639][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:36.642][rule$waitAsNeeded] Wait 0.0364652 second(s).
biodb.TRACE[2022-10-18 22:25:36.687][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 22:25:37.006][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:37.008][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:37.009][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:37.010][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 22:25:37.644][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:37.646][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:37.647][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:37.649][rule$waitAsNeeded] Wait 0.0371201 second(s).
biodb.TRACE[2022-10-18 22:25:37.702][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 22:25:38.025][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:38.026][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:38.028][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:38.029][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 22:25:38.643][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:38.645][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:38.646][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:38.648][rule$waitAsNeeded] Wait 0.0536299 second(s).
biodb.TRACE[2022-10-18 22:25:38.718][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 22:25:39.046][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:39.048][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:39.050][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:39.052][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 22:25:39.667][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:39.670][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:39.672][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:39.674][rule$waitAsNeeded] Wait 0.043752 second(s).
biodb.TRACE[2022-10-18 22:25:39.734][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 22:25:40.057][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:40.060][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:40.062][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:40.064][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 22:25:40.683][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:40.684][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:40.686][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:40.687][rule$waitAsNeeded] Wait 0.04581 second(s).
biodb.TRACE[2022-10-18 22:25:40.749][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 22:25:41.063][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:41.064][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:41.066][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:41.068][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 22:25:41.681][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:41.683][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:41.684][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:41.685][rule$waitAsNeeded] Wait 0.0630109 second(s).
biodb.TRACE[2022-10-18 22:25:41.765][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 22:25:42.082][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:42.084][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:42.085][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:42.087][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 22:25:42.696][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:42.698][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:42.700][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:42.702][rule$waitAsNeeded] Wait 0.0628109 second(s).
biodb.TRACE[2022-10-18 22:25:42.781][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 22:25:43.106][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:43.108][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:43.109][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:43.111][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 22:25:43.735][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:43.736][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:43.738][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:43.739][rule$waitAsNeeded] Wait 0.040765 second(s).
biodb.TRACE[2022-10-18 22:25:43.796][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 22:25:44.119][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:44.120][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:44.122][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:44.123][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 22:25:44.719][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:44.721][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:44.722][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:44.723][rule$waitAsNeeded] Wait 0.0724411 second(s).
biodb.TRACE[2022-10-18 22:25:44.812][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2022-10-18 22:25:45.128][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:45.129][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:45.131][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:45.132][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2022-10-18 22:25:45.738][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2022-10-18 22:25:45.765][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2022-10-18 22:25:45.771][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 22:25:45.787][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2022-10-18 22:25:45.789][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 22:25:45.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:45.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:45.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:45.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:45.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:45.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:45.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:45.806][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:45.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:45.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:45.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:45.811][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:45.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:45.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:45.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:45.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:45.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:45.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:45.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:45.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:45.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:45.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:45.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:45.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:45.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:45.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:45.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:45.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:45.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:45.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:45.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:45.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:45.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:45.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:45.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:45.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:45.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:45.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:45.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:25:45.847][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2022-10-18 22:25:45.848][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2022-10-18 22:25:45.857][biodb::testThat]
biodb.INFO [2022-10-18 22:25:45.858][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2022-10-18 22:25:45.860][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:25:45.861][biodb::testThat]
biodb.DEBUG[2022-10-18 22:25:45.869][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2022-10-18 22:25:45.871][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2022-10-18 22:25:45.872][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-10-18 22:25:45.874][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2022-10-18 22:25:45.876][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-10-18 22:25:45.878][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 22:25:45.879][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 22:25:45.881][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 22:25:45.882][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 22:25:45.883][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 22:25:45.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:45.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:45.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:45.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:45.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:45.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:45.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:25:45.902][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2022-10-18 22:25:45.905][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:45.907][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:25:45.908][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 22:25:46.220][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:46.221][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:46.223][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:46.224][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 22:25:46.845][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:46.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:46.848][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:46.849][rule$waitAsNeeded] Wait 0.0587111 second(s).
biodb.TRACE[2022-10-18 22:25:46.921][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 22:25:47.239][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:47.240][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:47.242][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:47.243][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 22:25:47.846][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:47.848][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:47.849][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:47.850][rule$waitAsNeeded] Wait 0.0703681 second(s).
biodb.TRACE[2022-10-18 22:25:47.937][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 22:25:48.257][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:48.258][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:48.260][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:48.261][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 22:25:48.875][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:48.877][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:48.879][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:48.881][rule$waitAsNeeded] Wait 0.055548 second(s).
biodb.TRACE[2022-10-18 22:25:48.953][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 22:25:49.283][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:49.284][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:49.286][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:49.287][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 22:25:49.903][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:49.905][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:49.907][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:49.909][rule$waitAsNeeded] Wait 0.0434411 second(s).
biodb.TRACE[2022-10-18 22:25:49.968][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 22:25:50.296][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:50.297][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:50.299][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:50.300][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 22:25:50.916][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:50.918][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:50.919][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:50.921][rule$waitAsNeeded] Wait 0.0471971 second(s).
biodb.TRACE[2022-10-18 22:25:50.985][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 22:25:51.360][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:51.361][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:51.363][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:51.364][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 22:25:51.981][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:51.983][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:51.985][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:25:51.987][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 22:25:52.317][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:52.318][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:52.320][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:52.321][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 22:25:52.931][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:52.932][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:52.934][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:52.935][rule$waitAsNeeded] Wait 0.051641 second(s).
biodb.TRACE[2022-10-18 22:25:53.000][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 22:25:53.325][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:53.327][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:53.330][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:53.332][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 22:25:53.958][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:53.960][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:53.962][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:53.965][rule$waitAsNeeded] Wait 0.035203 second(s).
biodb.TRACE[2022-10-18 22:25:54.016][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 22:25:54.357][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:54.358][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:54.360][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:54.361][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 22:25:54.992][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:54.994][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:54.995][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:54.997][rule$waitAsNeeded] Wait 0.018352 second(s).
biodb.TRACE[2022-10-18 22:25:55.031][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2022-10-18 22:25:55.346][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:55.348][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:55.349][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:55.351][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2022-10-18 22:25:55.956][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2022-10-18 22:25:55.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:55.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:55.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:55.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:55.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:55.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:55.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:25:55.973][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.INFO [2022-10-18 22:25:55.976][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.DEBUG[2022-10-18 22:25:55.978][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:55.979][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:25:55.980][rule$waitAsNeeded] Wait 0.050462 second(s).
biodb.TRACE[2022-10-18 22:25:56.047][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2022-10-18 22:25:56.361][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:25:56.363][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:56.364][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:56.366][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2022-10-18 22:25:57.020][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:25:57.030][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2022-10-18 22:25:57.045][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2022-10-18 22:25:57.060][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2022-10-18 22:25:57.068][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 22:25:57.094][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-10-18 22:25:57.097][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 22:25:57.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:57.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:57.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:57.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:57.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:57.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:57.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:57.114][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:57.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:57.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.120][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:57.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:57.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:25:57.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:25:57.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:25:57.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:25:57.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:25:57.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:25:57.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:25:57.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:25:57.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:25:57.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:25:57.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:25:57.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:25:57.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.197][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:25:57.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:25:57.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.203][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:25:57.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:25:57.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.212][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:25:57.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:25:57.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.217][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:25:57.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:25:57.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.226][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:25:57.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:25:57.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.231][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:25:57.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:25:57.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.240][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:25:57.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:25:57.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.245][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:25:57.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:25:57.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.254][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:25:57.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:57.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.259][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:25:57.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:25:57.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.268][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:25:57.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:25:57.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.273][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:25:57.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:25:57.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:57.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:57.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.287][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:57.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:57.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.296][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:25:57.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:57.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.301][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 22:25:57.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:57.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:57.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:57.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:57.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:57.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.316][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:25:57.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:57.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:57.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:57.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.330][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:57.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:57.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:57.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:57.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:57.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:57.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.345][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:25:57.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:25:57.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.353][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:57.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:57.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.359][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:57.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:57.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.368][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:57.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:25:57.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:25:57.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:25:57.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:25:57.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:25:57.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:25:57.434][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2022-10-18 22:25:57.435][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2022-10-18 22:25:57.437][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2022-10-18 22:25:57.453][biodb::testThat]
biodb.INFO [2022-10-18 22:25:57.454][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2022-10-18 22:25:57.455][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:25:57.457][biodb::testThat]
biodb.INFO [2022-10-18 22:25:57.481][biodb::testThat]
biodb.INFO [2022-10-18 22:25:57.482][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2022-10-18 22:25:57.483][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:25:57.485][biodb::testThat]
biodb.INFO [2022-10-18 22:25:57.495][biodb::testThat]
biodb.INFO [2022-10-18 22:25:57.496][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2022-10-18 22:25:57.497][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:25:57.499][biodb::testThat]
biodb.DEBUG[2022-10-18 22:25:57.592][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2022-10-18 22:25:57.596][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:25:57.597][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:25:57.599][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2022-10-18 22:25:57.912][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV does not exist.
biodb.TRACE[2022-10-18 22:25:57.914][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:25:57.916][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:25:57.919][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2022-10-18 22:26:03.908][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:26:03.918][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2022-10-18 22:26:04.023][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2022-10-18 22:26:06.756][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:06.757][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:06.759][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:06.760][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:06.761][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:06.762][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:06.763][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:06.764][ef$get] fields variable is a list.
biodb.INFO [2022-10-18 22:26:06.767][biodb::testThat]
biodb.INFO [2022-10-18 22:26:06.768][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2022-10-18 22:26:06.769][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:26:06.770][biodb::testThat]
biodb.ERROR[2022-10-18 22:26:06.786][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2022-10-18 22:26:06.799][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2022-10-18 22:26:06.807][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 22:26:06.808][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-10-18 22:26:06.810][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-10-18 22:26:06.811][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 22:26:06.812][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:07.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:07.253][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.256][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 22:26:07.270][biodb::testContext]
biodb.INFO [2022-10-18 22:26:07.272][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 22:26:07.274][biodb::testContext] Test context - Web services tests
biodb.INFO [2022-10-18 22:26:07.276][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 22:26:07.278][biodb::testContext]
biodb.INFO [2022-10-18 22:26:07.288][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 22:26:07.292][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 22:26:07.301][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 22:26:07.303][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 22:26:07.305][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 22:26:07.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.313][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 22:26:07.315][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 22:26:07.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.322][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 22:26:07.324][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 22:26:07.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.331][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 22:26:07.333][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 22:26:07.335][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 22:26:07.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.342][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 22:26:07.344][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 22:26:07.346][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 22:26:07.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.354][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 22:26:07.356][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 22:26:07.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.363][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 22:26:07.365][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 22:26:07.367][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 22:26:07.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.374][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 22:26:07.376][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 22:26:07.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.386][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 22:26:07.388][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 22:26:07.390][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 22:26:07.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.397][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 22:26:07.399][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 22:26:07.401][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 22:26:07.404][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 22:26:07.406][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 22:26:07.409][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 22:26:07.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.416][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 22:26:07.418][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 22:26:07.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.425][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[2022-10-18 22:26:07.427][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 22:26:07.430][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 22:26:07.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.440][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 22:26:07.443][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 22:26:07.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.451][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 22:26:07.455][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 22:26:07.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.461][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 22:26:07.463][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 22:26:07.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.470][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 22:26:07.475][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 22:26:07.479][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 22:26:07.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.485][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 22:26:07.487][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 22:26:07.488][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 22:26:07.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.495][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 22:26:07.498][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:07.499][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 22:26:07.503][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.505][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:26:07.506][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.507][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:26:07.509][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:07.510][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:26:07.511][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 22:26:07.513][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:26:07.514][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.515][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 22:26:07.517][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:26:07.520][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.521][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.523][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 22:26:07.523][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 22:26:07.523][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 22:26:07.523][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 22:26:07.523][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 22:26:07.525][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:26:07.526][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:07.528][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:07.533][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:26:07.535][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:07.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:07.538][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:26:07.539][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.541][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:26:07.542][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:26:07.543][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:07.545][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.547][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 22:26:07.551][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:07.553][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 22:26:07.554][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.555][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:26:07.557][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.558][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:26:07.559][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:07.561][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:26:07.562][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 22:26:07.564][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:26:07.565][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.567][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 22:26:07.568][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:26:07.569][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.571][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.572][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 22:26:07.572][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 22:26:07.572][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 22:26:07.572][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 22:26:07.572][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 22:26:07.574][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:26:07.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:07.577][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:07.578][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:26:07.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:07.581][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:07.583][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:26:07.584][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.586][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:26:07.587][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:26:07.588][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:07.590][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.591][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 22:26:07.594][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.596][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 22:26:07.600][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.602][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:26:07.604][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.605][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:26:07.607][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:07.608][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:26:07.610][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 22:26:07.612][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:26:07.614][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:07.616][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 22:26:07.617][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:26:07.618][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.620][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.621][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.623][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:26:07.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:07.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:07.628][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:26:07.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:07.631][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:07.633][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:26:07.634][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.636][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:26:07.638][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:26:07.640][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:07.642][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.645][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 22:26:07.648][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.650][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 22:26:07.652][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.654][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:26:07.656][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.658][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:26:07.660][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:07.662][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:26:07.664][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 22:26:07.666][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:26:07.668][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:07.670][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 22:26:07.671][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:26:07.673][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.675][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:07.677][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.679][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:26:07.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:07.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:07.684][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:26:07.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:07.688][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:07.690][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:26:07.717][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.719][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:26:07.721][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:26:07.723][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:07.725][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:07.727][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 22:26:07.729][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.776][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[2022-10-18 22:26:07.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.827][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[2022-10-18 22:26:07.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:07.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:07.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:07.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:07.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:07.840][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 22:26:07.841][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 22:26:07.843][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 22:26:07.845][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 22:26:07.846][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 22:26:07.848][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 22:26:07.849][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 22:26:07.851][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 22:26:07.852][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 22:26:07.854][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 22:26:07.856][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 22:26:07.857][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 22:26:07.859][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 22:26:07.860][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 22:26:07.863][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 22:26:07.865][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 22:26:07.867][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 22:26:07.870][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 22:26:07.872][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 22:26:07.874][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 22:26:07.876][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 22:26:07.878][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 22:26:07.879][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 22:26:07.881][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 22:26:07.883][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 22:26:07.885][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 22:26:07.887][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 22:26:07.890][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 22:26:07.893][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 22:26:07.895][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 22:26:07.897][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 22:26:07.898][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 22:26:07.900][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 22:26:07.902][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 22:26:07.904][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 22:26:07.906][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 22:26:07.908][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 22:26:07.909][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 22:26:07.911][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 22:26:07.913][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 22:26:07.915][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 22:26:07.917][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 22:26:07.920][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 22:26:07.922][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 22:26:07.924][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 22:26:07.926][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 22:26:07.928][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 22:26:07.930][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 22:26:07.933][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 22:26:07.935][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 22:26:07.938][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 22:26:07.940][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 22:26:07.943][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 22:26:07.946][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 22:26:07.948][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 22:26:07.951][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 22:26:07.953][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 22:26:07.956][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 22:26:07.958][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 22:26:07.960][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 22:26:07.961][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 22:26:07.963][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 22:26:07.964][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 22:26:07.966][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 22:26:07.968][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 22:26:07.969][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 22:26:07.971][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 22:26:07.973][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 22:26:07.975][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 22:26:07.977][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 22:26:07.978][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 22:26:07.980][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 22:26:07.982][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 22:26:07.984][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 22:26:07.986][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 22:26:07.988][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 22:26:07.990][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 22:26:07.993][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 22:26:07.995][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 22:26:07.998][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 22:26:08.000][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 22:26:08.003][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 22:26:08.005][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 22:26:08.008][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 22:26:08.011][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 22:26:08.013][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 22:26:08.015][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.017][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.065][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[2022-10-18 22:26:08.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.082][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[2022-10-18 22:26:08.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:08.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:08.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:08.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:08.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:08.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:08.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:08.200][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.15-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-10-18 22:26:08.203][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 22:26:08.205][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:08.206][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 22:26:08.207][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:08.209][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:26:08.210][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:08.211][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:26:08.212][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:08.214][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:26:08.215][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 22:26:08.216][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:26:08.217][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:08.219][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-10-18 22:26:08.220][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:26:08.221][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-10-18 22:26:08.221][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-10-18 22:26:08.221][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-10-18 22:26:08.221][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-10-18 22:26:08.221][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-10-18 22:26:08.221][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-10-18 22:26:08.221][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-10-18 22:26:08.221][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-10-18 22:26:08.221][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-10-18 22:26:08.223][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:08.224][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 22:26:08.224][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 22:26:08.225][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:26:08.227][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:08.228][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:08.229][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:26:08.230][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:08.231][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:08.233][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:26:08.234][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 22:26:08.234][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-10-18 22:26:08.235][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:26:08.236][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:26:08.237][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:08.239][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:08.241][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-10-18 22:26:08.243][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 22:26:08.246][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 22:26:08.247][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-10-18 22:26:08.249][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 22:26:08.251][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-10-18 22:26:08.252][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 22:26:08.253][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 22:26:08.255][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-10-18 22:26:08.257][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-10-18 22:26:08.259][biodb::testThat]
biodb.INFO [2022-10-18 22:26:08.261][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2022-10-18 22:26:08.263][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:26:08.264][biodb::testThat]
biodb.DEBUG[2022-10-18 22:26:08.343][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2022-10-18 22:26:08.350][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:26:08.351][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:26:08.353][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2022-10-18 22:26:08.668][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride does not exist.
biodb.TRACE[2022-10-18 22:26:08.670][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:26:08.673][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:26:08.675][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2022-10-18 22:26:09.329][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:26:09.342][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2022-10-18 22:26:09.360][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2022-10-18 22:26:09.481][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2022-10-18 22:26:09.485][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:26:09.486][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:26:09.488][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2022-10-18 22:26:09.802][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty does not exist.
biodb.TRACE[2022-10-18 22:26:09.805][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:26:09.809][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:26:09.812][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2022-10-18 22:26:10.607][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:26:10.622][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2022-10-18 22:26:10.644][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2022-10-18 22:26:10.662][biodb::testThat]
biodb.INFO [2022-10-18 22:26:10.663][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2022-10-18 22:26:10.665][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:26:10.666][biodb::testThat]
biodb.INFO [2022-10-18 22:26:10.704][biodb::testThat]
biodb.INFO [2022-10-18 22:26:10.706][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2022-10-18 22:26:10.708][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:26:10.710][biodb::testThat]
biodb.DEBUG[2022-10-18 22:26:10.827][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2022-10-18 22:26:10.832][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:26:10.834][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:26:10.837][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2022-10-18 22:26:11.158][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001 does not exist.
biodb.TRACE[2022-10-18 22:26:11.160][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:26:11.162][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:26:11.163][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2022-10-18 22:26:11.584][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:26:11.593][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2022-10-18 22:26:11.611][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2022-10-18 22:26:11.715][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2022-10-18 22:26:11.718][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 22:26:11.720][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2022-10-18 22:26:11.722][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 22:26:11.724][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2022-10-18 22:26:11.798][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2022-10-18 22:26:11.802][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:26:11.803][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:26:11.805][rule$waitAsNeeded] Wait 0.0317409 second(s).
biodb.TRACE[2022-10-18 22:26:11.845][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2022-10-18 22:26:12.162][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001 does not exist.
biodb.TRACE[2022-10-18 22:26:12.164][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:26:12.167][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:26:12.170][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2022-10-18 22:26:12.598][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:26:12.608][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2022-10-18 22:26:12.629][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2022-10-18 22:26:12.731][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2022-10-18 22:26:12.736][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:26:12.737][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2022-10-18 22:26:12.739][rule$waitAsNeeded] Wait 0.105657 second(s).
biodb.TRACE[2022-10-18 22:26:12.862][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2022-10-18 22:26:13.208][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid does not exist.
biodb.TRACE[2022-10-18 22:26:13.210][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:26:13.213][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:26:13.215][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2022-10-18 22:26:14.814][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:26:14.825][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2022-10-18 22:26:14.857][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2022-10-18 22:26:15.468][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2022-10-18 22:26:15.472][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:26:15.474][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:26:15.476][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2022-10-18 22:26:15.793][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6 does not exist.
biodb.TRACE[2022-10-18 22:26:15.794][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:26:15.796][getUrlRequestResult] URL "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:26:15.798][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2022-10-18 22:26:17.350][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:26:17.365][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2022-10-18 22:26:17.407][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2022-10-18 22:26:17.847][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 22:26:17.849][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-10-18 22:26:17.850][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-10-18 22:26:17.852][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 22:26:17.853][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:17.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:17.856][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:17.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:17.859][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-18 22:26:17.866][biodb::testContext]
biodb.INFO [2022-10-18 22:26:17.869][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 22:26:17.871][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2022-10-18 22:26:17.872][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-18 22:26:17.873][biodb::testContext]
biodb.INFO [2022-10-18 22:26:17.881][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-18 22:26:17.884][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-18 22:26:17.889][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 22:26:17.890][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-18 22:26:17.892][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-18 22:26:17.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.897][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-18 22:26:17.898][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-18 22:26:17.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.902][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-18 22:26:17.904][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-18 22:26:17.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.908][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-18 22:26:17.910][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-18 22:26:17.911][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-18 22:26:17.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.916][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-18 22:26:17.918][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-18 22:26:17.919][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-18 22:26:17.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.923][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-18 22:26:17.924][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-18 22:26:17.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.930][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-18 22:26:17.932][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-18 22:26:17.934][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-18 22:26:17.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.939][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-18 22:26:17.941][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-18 22:26:17.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.945][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-18 22:26:17.946][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-18 22:26:17.948][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-18 22:26:17.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.954][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-18 22:26:17.955][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-18 22:26:17.957][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-18 22:26:17.959][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-18 22:26:17.960][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-18 22:26:17.961][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-18 22:26:17.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.966][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-18 22:26:17.967][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-18 22:26:17.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.972][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-18 22:26:17.973][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-18 22:26:17.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.978][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-18 22:26:17.979][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-18 22:26:17.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:17.984][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-18 22:26:17.985][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-18 22:26:17.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:17.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:17.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.016][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-18 22:26:18.018][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-18 22:26:18.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.025][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-18 22:26:18.027][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-18 22:26:18.033][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-18 22:26:18.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.040][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-18 22:26:18.042][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-18 22:26:18.044][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-18 22:26:18.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.048][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-18 22:26:18.050][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.052][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-18 22:26:18.053][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.054][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:26:18.055][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.057][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.058][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.059][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.060][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 22:26:18.062][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:26:18.063][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.064][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-18 22:26:18.065][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:26:18.066][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.068][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.069][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 22:26:18.069][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 22:26:18.069][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 22:26:18.069][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 22:26:18.069][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 22:26:18.070][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:26:18.071][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:18.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:18.074][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:26:18.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:18.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:18.077][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.078][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:26:18.081][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:26:18.082][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.083][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.084][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-18 22:26:18.086][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.087][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 22:26:18.089][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.090][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:26:18.091][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.093][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.094][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.095][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.097][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 22:26:18.098][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:26:18.100][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.101][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-18 22:26:18.102][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:26:18.103][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.104][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.106][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 22:26:18.106][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 22:26:18.106][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-18 22:26:18.106][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-18 22:26:18.106][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-18 22:26:18.107][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:26:18.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:18.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:18.111][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:26:18.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:18.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:18.116][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.117][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.118][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:26:18.119][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:26:18.121][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.122][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.123][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-18 22:26:18.126][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.127][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-18 22:26:18.128][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.130][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:26:18.131][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.132][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.133][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.134][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.136][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 22:26:18.137][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:26:18.138][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.139][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-18 22:26:18.141][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:26:18.142][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.143][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.144][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.146][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:26:18.147][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:18.148][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:18.149][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:26:18.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:18.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:18.153][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.154][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.155][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:26:18.156][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:26:18.157][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.158][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.160][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-18 22:26:18.162][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.163][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-18 22:26:18.164][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.166][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:26:18.167][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.168][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.169][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.171][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.172][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-18 22:26:18.173][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:26:18.175][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.176][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-18 22:26:18.177][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:26:18.178][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.179][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.181][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.182][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:26:18.183][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:18.184][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:18.186][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:26:18.187][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:18.188][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:18.189][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.191][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.192][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:26:18.193][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:26:18.194][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.195][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.197][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 22:26:18.198][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.308][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[2022-10-18 22:26:18.310][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-18 22:26:18.311][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-18 22:26:18.313][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-18 22:26:18.315][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-18 22:26:18.317][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-18 22:26:18.318][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-18 22:26:18.320][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-18 22:26:18.322][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-18 22:26:18.323][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-18 22:26:18.325][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-18 22:26:18.327][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-18 22:26:18.328][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-18 22:26:18.330][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-18 22:26:18.332][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-18 22:26:18.334][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-18 22:26:18.336][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 22:26:18.338][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-18 22:26:18.339][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-18 22:26:18.341][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-18 22:26:18.343][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-18 22:26:18.345][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-18 22:26:18.347][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-18 22:26:18.349][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-18 22:26:18.351][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-18 22:26:18.352][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-18 22:26:18.354][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-18 22:26:18.356][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-18 22:26:18.358][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-18 22:26:18.359][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-18 22:26:18.361][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-18 22:26:18.363][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-18 22:26:18.365][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-18 22:26:18.367][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-18 22:26:18.368][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-18 22:26:18.370][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-18 22:26:18.371][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-18 22:26:18.373][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-18 22:26:18.375][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-18 22:26:18.377][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-18 22:26:18.379][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-18 22:26:18.381][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-18 22:26:18.383][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-18 22:26:18.385][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-18 22:26:18.387][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-18 22:26:18.388][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-18 22:26:18.390][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-18 22:26:18.392][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-18 22:26:18.394][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-18 22:26:18.395][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-18 22:26:18.397][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-18 22:26:18.398][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-18 22:26:18.400][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-18 22:26:18.417][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-18 22:26:18.419][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-18 22:26:18.421][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-18 22:26:18.423][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-18 22:26:18.424][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-18 22:26:18.426][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-18 22:26:18.427][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-18 22:26:18.429][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-18 22:26:18.431][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-18 22:26:18.432][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-18 22:26:18.434][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-18 22:26:18.435][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-18 22:26:18.437][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-18 22:26:18.439][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-18 22:26:18.440][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-18 22:26:18.442][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-18 22:26:18.443][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-18 22:26:18.445][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-18 22:26:18.446][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-18 22:26:18.448][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-18 22:26:18.450][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-18 22:26:18.451][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-18 22:26:18.453][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-18 22:26:18.454][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-18 22:26:18.456][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-18 22:26:18.457][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-18 22:26:18.459][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-18 22:26:18.461][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-18 22:26:18.462][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-18 22:26:18.464][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-18 22:26:18.465][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-18 22:26:18.467][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-18 22:26:18.469][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-18 22:26:18.471][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-18 22:26:18.472][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.474][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-18 22:26:18.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:18.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:18.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:18.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:18.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:18.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:18.613][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.15-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2022-10-18 22:26:18.615][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 22:26:18.617][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.618][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.619][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.621][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-18 22:26:18.622][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.624][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.625][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.627][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.629][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-18 22:26:18.630][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-18 22:26:18.632][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.633][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2022-10-18 22:26:18.634][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-18 22:26:18.636][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2022-10-18 22:26:18.636][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2022-10-18 22:26:18.636][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2022-10-18 22:26:18.636][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2022-10-18 22:26:18.636][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2022-10-18 22:26:18.636][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2022-10-18 22:26:18.636][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2022-10-18 22:26:18.636][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2022-10-18 22:26:18.636][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2022-10-18 22:26:18.637][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-18 22:26:18.638][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-18 22:26:18.638][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-18 22:26:18.639][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-18 22:26:18.640][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:18.642][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:18.643][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-18 22:26:18.644][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-18 22:26:18.645][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-18 22:26:18.646][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-18 22:26:18.647][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 22:26:18.647][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2022-10-18 22:26:18.649][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-18 22:26:18.650][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-18 22:26:18.651][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-18 22:26:18.652][self$setPropertyValue]
biodb.DEBUG[2022-10-18 22:26:18.654][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2022-10-18 22:26:18.655][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-18 22:26:18.659][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 22:26:18.660][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2022-10-18 22:26:18.661][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2022-10-18 22:26:18.663][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2022-10-18 22:26:18.665][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 22:26:18.666][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2022-10-18 22:26:18.667][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2022-10-18 22:26:18.669][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2022-10-18 22:26:18.671][biodb::testThat]
biodb.INFO [2022-10-18 22:26:18.672][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2022-10-18 22:26:18.673][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-18 22:26:18.674][biodb::testThat]
biodb.DEBUG[2022-10-18 22:26:19.041][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2022-10-18 22:26:19.048][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2022-10-18 22:26:19.051][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2022-10-18 22:26:19.054][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2022-10-18 22:26:19.162][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2022-10-18 22:26:21.983][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2022-10-18 22:26:21.985][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2022-10-18 22:26:21.987][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2022-10-18 22:26:21.989][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2022-10-18 22:26:21.991][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2022-10-18 22:26:21.992][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2022-10-18 22:26:21.993][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2022-10-18 22:26:21.995][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2022-10-18 22:26:21.996][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2022-10-18 22:26:22.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:26:22.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:22.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:22.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:22.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:22.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:22.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:22.016][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2022-10-18 22:26:22.019][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:26:22.020][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:26:22.022][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2022-10-18 22:26:22.341][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:26:22.343][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:26:22.344][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:26:22.346][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2022-10-18 22:26:23.009][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:26:23.025][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2022-10-18 22:26:23.047][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.DEBUG[2022-10-18 22:26:23.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:26:23.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:23.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:23.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:23.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:23.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:23.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-18 22:26:23.078][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2022-10-18 22:26:23.082][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2022-10-18 22:26:23.083][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2022-10-18 22:26:23.086][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2022-10-18 22:26:23.406][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2022-10-18 22:26:23.407][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2022-10-18 22:26:23.409][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2022-10-18 22:26:23.411][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2022-10-18 22:26:24.040][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2022-10-18 22:26:24.052][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2022-10-18 22:26:24.069][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.TRACE[2022-10-18 22:26:24.085][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv"
biodb.DEBUG[2022-10-18 22:26:24.092][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2022-10-18 22:26:24.111][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2022-10-18 22:26:24.113][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2022-10-18 22:26:24.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:26:24.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:24.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:24.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:24.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:24.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:24.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:26:24.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.173][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:26:24.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:26:24.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.181][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:26:24.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:26:24.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.189][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.197][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.211][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.220][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.230][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:26:24.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.236][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:26:24.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.246][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:24.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:24.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.252][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:24.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:24.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.277][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:26:24.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.282][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 22:26:24.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.287][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.291][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.296][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:26:24.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.348][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.358][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.367][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.372][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.381][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:26:24.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:26:24.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:24.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:24.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:24.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:24.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:24.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:26:24.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.459][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:26:24.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2022-10-18 22:26:24.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.464][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:26:24.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2022-10-18 22:26:24.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.469][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.474][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.490][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.503][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:26:24.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.509][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2022-10-18 22:26:24.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.519][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:24.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:24.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.523][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:24.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:24.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.536][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.558][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:26:24.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.565][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2022-10-18 22:26:24.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.588][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2022-10-18 22:26:24.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.601][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.609][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.625][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-18 22:26:24.691][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2022-10-18 22:26:24.693][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2022-10-18 22:26:24.695][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:26:24.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:24.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:24.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:24.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:24.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:24.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:26:24.711][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 22:26:24.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 22:26:24.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.716][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 22:26:24.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 22:26:24.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.723][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 22:26:24.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 22:26:24.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.729][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 22:26:24.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 22:26:24.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.736][private$selectFields] Fields none
biodb.TRACE[2022-10-18 22:26:24.738][private$selectFields]
biodb.TRACE[2022-10-18 22:26:24.739][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-10-18 22:26:24.740][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 22:26:24.742][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:26:24.743][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.745][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.746][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.747][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.748][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.750][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.751][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.752][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.754][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.755][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.756][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.758][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.759][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.760][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.762][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.763][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.764][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.766][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.767][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.768][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.769][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:24.771][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:24.772][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.774][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.775][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.777][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.778][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.780][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.781][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.782][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.784][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.785][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.787][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.788][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.789][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.791][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.792][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.793][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.795][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.796][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.798][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.799][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.801][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.802][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.804][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.806][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.817][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.818][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.820][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.821][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.822][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.824][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.825][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:24.826][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:24.828][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.829][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.830][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.831][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.833][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.834][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.835][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.836][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.838][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.839][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.840][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:26:24.841][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:26:24.843][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.845][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.846][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.847][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.848][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.850][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.852][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.854][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.856][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.858][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.860][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.862][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.863][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.865][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.867][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.868][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.869][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.871][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.872][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.873][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.875][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:24.877][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:24.879][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.880][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.882][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:24.884][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:24.886][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.888][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.890][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.892][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:24.894][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.895][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.897][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2022-10-18 22:26:24.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:24.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:24.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:24.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.938][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.943][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.948][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:24.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.953][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.958][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.964][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:24.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:24.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.985][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:24.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:24.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.990][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:24.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:24.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:24.995][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:24.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:24.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:24.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:25.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:25.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:25.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:25.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:25.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:25.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.016][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.021][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.025][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.036][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2022-10-18 22:26:25.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-18 22:26:25.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:25.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:25.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:25.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:25.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:25.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-18 22:26:25.052][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 22:26:25.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 22:26:25.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.057][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-18 22:26:25.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-18 22:26:25.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.063][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-18 22:26:25.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-18 22:26:25.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.069][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-18 22:26:25.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-18 22:26:25.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.075][private$selectFields] Fields none
biodb.TRACE[2022-10-18 22:26:25.077][private$selectFields]
biodb.TRACE[2022-10-18 22:26:25.078][private$selectFields] Fields is null: TRUE
biodb.TRACE[2022-10-18 22:26:25.079][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2022-10-18 22:26:25.081][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:26:25.082][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:25.084][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:25.085][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.087][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.088][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:25.089][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:25.091][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.092][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.093][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:25.094][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:25.095][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.097][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.098][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:25.099][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:25.100][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.101][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.102][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:25.104][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:25.105][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.106][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.107][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:25.109][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:25.111][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.112][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.113][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:25.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:25.116][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.117][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.118][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.119][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.121][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.122][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.123][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:25.124][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:25.125][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.127][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.128][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:25.129][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:25.130][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.131][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.132][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:25.134][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:25.135][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.136][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.137][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:25.138][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:25.140][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.141][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.142][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:25.143][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:25.144][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.145][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.146][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:25.148][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:25.149][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.150][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.151][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:25.152][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:25.154][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.155][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.156][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.157][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.158][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.159][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.161][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:26:25.162][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2022-10-18 22:26:25.163][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:25.164][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:25.165][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.166][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.168][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:25.169][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:25.170][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.171][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.172][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:25.174][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:25.175][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.176][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.177][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:25.178][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:25.179][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.180][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.182][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:25.183][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:25.184][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.185][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.186][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:25.187][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:25.189][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.190][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.191][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:25.192][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:25.193][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.195][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.196][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.197][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.198][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.199][ef$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.200][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2022-10-18 22:26:25.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:25.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:25.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:25.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:25.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-18 22:26:25.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-18 22:26:25.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:25.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:25.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:25.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:25.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2022-10-18 22:26:25.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2022-10-18 22:26:25.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.231][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:25.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:25.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.249][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:25.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:25.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.254][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:25.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2022-10-18 22:26:25.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.259][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:25.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:25.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.263][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:25.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:25.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.268][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:25.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2022-10-18 22:26:25.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:25.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:25.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:25.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:25.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:25.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2022-10-18 22:26:25.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.287][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:25.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:25.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.292][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:25.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:25.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.297][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-18 22:26:25.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-18 22:26:25.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:25.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:25.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:25.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:25.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-18 22:26:25.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-18 22:26:25.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.316][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.321][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.325][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2022-10-18 22:26:25.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-18 22:26:25.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-18 22:26:25.334][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2022-10-18 22:26:25.335][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2022-10-18 22:26:25.336][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2022-10-18 22:26:25.339][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-18 22:26:25.340][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2022-10-18 22:26:25.342][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2022-10-18 22:26:25.343][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-18 22:26:25.344][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-18 22:26:25.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-18 22:26:25.346][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-18 22:26:25.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-18 22:26:25.348][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-18 22:26:25.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 169 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 169 ]
> 
> proc.time()
   user  system elapsed 
  44.32    1.65  104.98

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.561.343.93
LipidmapsStructureEntry0.770.000.76