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This page was generated on 2024-10-15 21:54 -0400 (Tue, 15 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4529
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4479
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

Package 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-10-13 14:00 -0400 (Sun, 13 Oct 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for biodbLipidmaps on merida1

To the developers/maintainers of the biodbLipidmaps package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbLipidmaps
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-10-14 01:29:45 -0400 (Mon, 14 Oct 2024)
EndedAt: 2024-10-14 01:35:14 -0400 (Mon, 14 Oct 2024)
EllapsedTime: 328.7 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbLipidmaps.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
LipidmapsStructureConn 4.909  1.979  19.061
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-10-14 01:33:01.557][biodb::testContext]
biodb.INFO [2024-10-14 01:33:01.579][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-14 01:33:01.582][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-14 01:33:01.585][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-14 01:33:01.601][biodb::testContext]
biodb.INFO [2024-10-14 01:33:01.646][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-14 01:33:01.651][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-14 01:33:01.693][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-14 01:33:01.707][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-14 01:33:01.732][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-14 01:33:01.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:01.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:01.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:01.755][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-14 01:33:01.947][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-14 01:33:01.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:01.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:01.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:01.964][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-14 01:33:01.967][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-14 01:33:01.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:01.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:01.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:01.989][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-14 01:33:01.992][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-14 01:33:02.001][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-14 01:33:02.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:02.018][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-14 01:33:02.020][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-14 01:33:02.035][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-14 01:33:02.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:02.065][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-14 01:33:02.068][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-14 01:33:02.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.096][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[2024-10-14 01:33:02.100][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-14 01:33:02.103][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-14 01:33:02.105][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-14 01:33:02.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:02.132][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-14 01:33:02.159][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-14 01:33:02.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:02.184][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-14 01:33:02.188][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-14 01:33:02.191][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-14 01:33:02.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:02.213][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-14 01:33:02.228][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-14 01:33:02.231][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-14 01:33:02.243][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-14 01:33:02.255][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-14 01:33:02.266][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-14 01:33:02.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.275][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[2024-10-14 01:33:02.287][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-14 01:33:02.290][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-14 01:33:02.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:02.305][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-14 01:33:02.308][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-14 01:33:02.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:02.336][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-14 01:33:02.339][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-14 01:33:02.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:02.364][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-14 01:33:02.382][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-14 01:33:02.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:02.405][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-14 01:33:02.409][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-14 01:33:02.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:02.430][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-14 01:33:02.433][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-14 01:33:02.475][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-14 01:33:02.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:02.493][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-14 01:33:02.496][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-14 01:33:02.498][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-14 01:33:02.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:02.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:02.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:02.548][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-14 01:33:02.752][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:02.870][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-14 01:33:02.875][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:02.878][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:33:02.893][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.050][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:33:03.053][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:03.056][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:33:03.058][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-14 01:33:03.061][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:33:03.066][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.069][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-14 01:33:03.071][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:33:03.074][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.077][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.080][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-14 01:33:03.080][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-14 01:33:03.080][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-14 01:33:03.080][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-14 01:33:03.080][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-14 01:33:03.083][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:33:03.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:33:03.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:33:03.093][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:33:03.095][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:33:03.098][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:33:03.100][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:33:03.103][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.106][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:33:03.109][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:33:03.111][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:03.114][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.121][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-14 01:33:03.127][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:03.130][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-14 01:33:03.147][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.150][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:33:03.153][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.156][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:33:03.170][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:03.173][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:33:03.176][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-14 01:33:03.190][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:33:03.193][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.196][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-14 01:33:03.210][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:33:03.218][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.221][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.224][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-14 01:33:03.224][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-14 01:33:03.224][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-14 01:33:03.224][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-14 01:33:03.224][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-14 01:33:03.227][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:33:03.230][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:33:03.233][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:33:03.247][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:33:03.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:33:03.292][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:33:03.308][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:33:03.311][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.314][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:33:03.316][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:33:03.332][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:03.338][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.351][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-14 01:33:03.356][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.371][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-14 01:33:03.374][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.378][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:33:03.391][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.394][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:33:03.397][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:03.400][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:33:03.413][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-14 01:33:03.419][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:33:03.423][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:03.436][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-14 01:33:03.439][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:33:03.441][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.456][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.459][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.462][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:33:03.476][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:33:03.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:33:03.482][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:33:03.486][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:33:03.508][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:33:03.514][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:33:03.517][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.521][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:33:03.534][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:33:03.537][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:03.539][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.554][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-14 01:33:03.562][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.565][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-14 01:33:03.582][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.585][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:33:03.587][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.590][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:33:03.602][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:03.604][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:33:03.607][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-14 01:33:03.609][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:33:03.615][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:03.617][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-14 01:33:03.620][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:33:03.623][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.638][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:03.641][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.643][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:33:03.646][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:33:03.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:33:03.659][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:33:03.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:33:03.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:33:03.679][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:33:03.681][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.684][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:33:03.704][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:33:03.720][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:03.723][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:03.738][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-14 01:33:03.741][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:03.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:03.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:03.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:03.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:03.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:03.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:03.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:03.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:03.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:03.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:03.820][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[2024-10-14 01:33:03.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:03.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:03.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:03.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:03.844][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[2024-10-14 01:33:03.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:03.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:03.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:03.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:03.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:03.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:03.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:03.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:03.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:03.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:03.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:03.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:03.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:03.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:03.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:03.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:03.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:03.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:03.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:03.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:03.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:03.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:03.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:03.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:03.969][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.DEBUG[2024-10-14 01:33:03.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:03.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:03.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:03.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:03.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:04.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:04.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:04.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:04.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:04.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:04.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:04.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:04.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:04.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:04.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:04.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:04.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:04.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:04.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:04.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:04.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:04.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:04.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:04.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:04.081][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[2024-10-14 01:33:04.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:04.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:04.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:04.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:04.104][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[2024-10-14 01:33:04.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:04.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:04.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:04.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:04.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:04.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:04.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:04.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:04.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:04.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:04.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:04.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:04.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:04.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:04.172][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[2024-10-14 01:33:04.175][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-14 01:33:04.197][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-14 01:33:04.203][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-14 01:33:04.232][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-14 01:33:04.237][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-14 01:33:04.240][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-14 01:33:04.264][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-14 01:33:04.267][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-14 01:33:04.277][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-14 01:33:04.285][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-14 01:33:04.290][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-14 01:33:04.306][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-14 01:33:04.309][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-14 01:33:04.313][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-14 01:33:04.329][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-14 01:33:04.333][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-14 01:33:04.347][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-14 01:33:04.351][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-14 01:33:04.356][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-14 01:33:04.370][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-14 01:33:04.374][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-14 01:33:04.388][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-14 01:33:04.393][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-14 01:33:04.411][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-14 01:33:04.415][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-14 01:33:04.426][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-14 01:33:04.431][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-14 01:33:04.446][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-14 01:33:04.455][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-14 01:33:04.459][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-14 01:33:04.463][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-14 01:33:04.480][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-14 01:33:04.484][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-14 01:33:04.503][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-14 01:33:04.508][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-14 01:33:04.512][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-14 01:33:04.531][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-14 01:33:04.534][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-14 01:33:04.556][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-14 01:33:04.560][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-14 01:33:04.566][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-14 01:33:04.570][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-14 01:33:04.583][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-14 01:33:04.587][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-14 01:33:04.604][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-14 01:33:04.608][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-14 01:33:04.612][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-14 01:33:04.632][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-14 01:33:04.637][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-14 01:33:04.641][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-14 01:33:04.657][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-14 01:33:04.661][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-14 01:33:04.667][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-14 01:33:04.671][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-14 01:33:04.675][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-14 01:33:04.707][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-14 01:33:04.711][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-14 01:33:04.714][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-14 01:33:04.733][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-14 01:33:04.736][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-14 01:33:04.752][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-14 01:33:04.756][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-14 01:33:04.759][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-14 01:33:04.775][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-14 01:33:04.780][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-14 01:33:04.783][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-14 01:33:04.796][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-14 01:33:04.800][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-14 01:33:04.803][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-14 01:33:04.820][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-14 01:33:04.823][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-14 01:33:04.839][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-14 01:33:04.843][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-14 01:33:04.847][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-14 01:33:04.863][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-14 01:33:04.866][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-14 01:33:04.870][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-14 01:33:04.883][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-14 01:33:04.887][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-14 01:33:04.892][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-14 01:33:04.916][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-14 01:33:04.919][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-14 01:33:04.922][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-14 01:33:04.942][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-14 01:33:04.946][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-14 01:33:04.955][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-14 01:33:04.957][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:04.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:04.966][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:04.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.172][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[2024-10-14 01:33:05.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.472][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[2024-10-14 01:33:05.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:33:05.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:05.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:05.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:05.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:05.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:05.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:05.644][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-14 01:33:05.725][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-14 01:33:05.742][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:05.746][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-14 01:33:05.748][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:05.750][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:33:05.765][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:05.768][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:33:05.770][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:05.772][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:33:05.788][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-14 01:33:05.791][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:33:05.794][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:05.796][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-14 01:33:05.808][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:33:05.812][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-14 01:33:05.812][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-14 01:33:05.812][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-14 01:33:05.812][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-14 01:33:05.812][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-14 01:33:05.812][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-14 01:33:05.812][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-14 01:33:05.812][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-14 01:33:05.812][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-14 01:33:05.816][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-14 01:33:05.819][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-14 01:33:05.819][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-14 01:33:05.835][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:33:05.838][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:33:05.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:33:05.843][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:33:05.858][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:33:05.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:33:05.862][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:33:05.865][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-14 01:33:05.865][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-14 01:33:05.879][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:33:05.881][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:33:05.884][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-14 01:33:05.886][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:33:05.930][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-14 01:33:05.947][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-14 01:33:06.001][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-14 01:33:06.003][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-14 01:33:06.019][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-14 01:33:06.038][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-14 01:33:06.047][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-14 01:33:06.050][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-14 01:33:06.053][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-14 01:33:06.057][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-14 01:33:06.103][biodb::testThat]
biodb.INFO [2024-10-14 01:33:06.119][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-10-14 01:33:06.121][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:06.122][biodb::testThat]
biodb.TRACE[2024-10-14 01:33:06.131][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-10-14 01:33:06.135][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-14 01:33:06.146][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-14 01:33:06.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:06.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:06.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:06.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:06.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:06.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:06.206][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.TRACE[2024-10-14 01:33:06.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:06.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:06.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:06.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:06.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:33:06.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:33:06.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.303][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:33:06.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:33:06.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.312][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:33:06.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:33:06.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.321][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:06.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:06.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.409][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:06.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:06.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.419][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:06.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:06.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.428][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:06.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:06.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.442][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:33:06.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:06.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.451][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:33:06.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:06.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.467][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:06.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:06.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.485][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:06.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:06.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:06.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:06.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:06.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:06.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.529][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:33:06.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:06.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.540][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-14 01:33:06.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:06.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:06.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:06.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:06.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:06.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.573][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:33:06.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:06.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:06.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:06.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.652][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:06.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:06.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:06.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:06.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:06.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:06.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:06.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:06.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.846][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:06.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:06.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.861][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:06.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:06.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:06.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:06.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.892][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:06.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:06.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:06.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:06.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:06.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:06.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:06.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:06.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:06.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:06.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:06.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:06.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:06.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:06.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:06.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:06.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:33:07.007][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-10-14 01:33:07.018][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-14 01:33:07.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-14 01:33:07.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.071][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-14 01:33:07.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-14 01:33:07.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.085][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-14 01:33:07.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-14 01:33:07.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.094][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-14 01:33:07.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-14 01:33:07.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:07.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:07.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.282][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:07.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:07.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:07.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:07.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:07.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:07.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:07.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:07.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:07.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:07.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:07.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:07.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:07.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:07.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.443][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:07.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:07.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.456][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:07.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:07.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.473][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:07.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:07.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:07.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:07.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:07.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:07.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:07.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:07.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.626][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:07.628][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:07.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.634][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:07.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:07.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:07.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:07.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.678][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:07.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:07.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.689][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:07.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:07.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.701][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:07.703][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:07.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.707][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:07.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:07.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.761][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:07.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:07.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.771][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:07.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:07.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.782][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:07.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:07.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.807][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:07.810][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:07.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.840][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.842][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:07.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:07.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.886][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:07.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:07.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.894][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:07.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:07.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.904][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:07.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:07.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.914][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:07.917][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:07.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.922][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:07.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:07.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:07.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:07.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:07.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:07.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:07.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:07.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:07.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:07.992][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:07.995][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:08.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.006][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:08.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:08.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.059][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.098][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.113][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.148][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.150][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.171][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.174][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.177][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.224][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:08.226][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:08.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.231][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.245][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:08.248][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:08.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.252][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.265][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:08.268][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:08.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.272][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.285][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:08.288][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:08.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.291][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.315][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:08.317][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:08.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.321][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.356][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.359][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.366][ef$get] fields variable is a list.
biodb.INFO [2024-10-14 01:33:08.396][biodb::testThat]
biodb.INFO [2024-10-14 01:33:08.398][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-14 01:33:08.400][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:08.403][biodb::testThat]
biodb.DEBUG[2024-10-14 01:33:08.450][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-10-14 01:33:08.466][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-14 01:33:08.472][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-10-14 01:33:08.482][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-14 01:33:08.486][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-10-14 01:33:08.489][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-14 01:33:08.568][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-14 01:33:08.578][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-14 01:33:08.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:08.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:08.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:08.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:08.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:08.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:08.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:33:08.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:08.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:08.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:08.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:08.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:33:08.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:33:08.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:33:08.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:33:08.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.663][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:33:08.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:33:08.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.674][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:33:08.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:33:08.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.683][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.695][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:08.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.706][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:08.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:08.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.717][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:08.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:08.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.731][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:33:08.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:08.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.746][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:33:08.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:08.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.755][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:08.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:08.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:08.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:08.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:08.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:08.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:08.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:08.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.807][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:33:08.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:08.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.827][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-14 01:33:08.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:08.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.838][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:08.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:08.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:08.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:08.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.919][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:33:08.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:08.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:08.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:08.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:08.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:08.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.949][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:08.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:08.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:08.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:08.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:08.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:09.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:09.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:09.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.026][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:09.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:09.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.035][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:09.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:09.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:09.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:09.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.059][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:09.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:09.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:09.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:09.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:09.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:09.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:09.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:09.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:09.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:09.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:09.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:09.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:09.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:09.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:33:09.162][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-10-14 01:33:09.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-14 01:33:09.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-14 01:33:09.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-14 01:33:09.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-14 01:33:09.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-14 01:33:09.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-14 01:33:09.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-14 01:33:09.347][biodb::testThat]
biodb.INFO [2024-10-14 01:33:09.350][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-14 01:33:09.352][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:09.355][biodb::testThat]
biodb.TRACE[2024-10-14 01:33:09.362][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:09.364][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:09.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.369][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:33:09.372][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-10-14 01:33:09.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:09.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:09.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:09.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:09.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:09.521][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:09.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:09.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:09.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:33:09.552][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-14 01:33:09.565][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[2024-10-14 01:33:09.700][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:33:09.702][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:33:09.712][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-10-14 01:33:10.563][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-10-14 01:33:10.939][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:33:10.951][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-10-14 01:33:11.081][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-10-14 01:33:11.116][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-10-14 01:33:11.142][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:11.145][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:11.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:11.149][ef$get] fields variable is a list.
biodb.INFO [2024-10-14 01:33:11.156][biodb::testThat]
biodb.INFO [2024-10-14 01:33:11.158][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-10-14 01:33:11.160][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:11.163][biodb::testThat]
biodb.TRACE[2024-10-14 01:33:11.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:11.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:11.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:11.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:11.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:11.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:11.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:11.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:11.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:11.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:11.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:11.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:33:11.642][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-14 01:33:11.647][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-14 01:33:11.677][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-14 01:33:11.680][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-14 01:33:11.692][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-10-14 01:33:11.729][biodb::testThat]
biodb.INFO [2024-10-14 01:33:11.731][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-10-14 01:33:11.733][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:11.736][biodb::testThat]
biodb.TRACE[2024-10-14 01:33:11.798][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-14 01:33:11.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-14 01:33:11.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:11.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:11.822][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-14 01:33:11.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-14 01:33:11.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:11.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:11.862][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-14 01:33:11.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-14 01:33:11.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:11.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:11.873][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-14 01:33:11.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-14 01:33:11.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:11.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:11.976][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-14 01:33:11.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-14 01:33:11.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:11.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:11.984][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-14 01:33:11.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-14 01:33:11.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:11.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:11.990][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-14 01:33:11.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-14 01:33:11.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:11.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:12.002][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-14 01:33:12.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-14 01:33:12.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:12.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-14 01:33:12.028][biodb::testThat]
biodb.INFO [2024-10-14 01:33:12.030][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-14 01:33:12.032][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:12.034][biodb::testThat]
biodb.INFO [2024-10-14 01:33:12.122][biodb::testThat]
biodb.INFO [2024-10-14 01:33:12.124][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-14 01:33:12.126][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:12.128][biodb::testThat]
biodb.INFO [2024-10-14 01:33:12.160][biodb::testThat]
biodb.INFO [2024-10-14 01:33:12.161][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-14 01:33:12.164][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:12.166][biodb::testThat]
biodb.DEBUG[2024-10-14 01:33:12.177][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-10-14 01:33:12.741][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-10-14 01:33:13.093][biodb::testThat]
biodb.INFO [2024-10-14 01:33:13.102][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-14 01:33:13.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:13.106][biodb::testThat]
biodb.TRACE[2024-10-14 01:33:13.117][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:13.119][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:13.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:13.123][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:13.124][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:13.125][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:13.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:13.128][ef$get] fields variable is a list.
biodb.INFO [2024-10-14 01:33:13.130][biodb::testThat]
biodb.INFO [2024-10-14 01:33:13.137][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-10-14 01:33:13.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:13.142][biodb::testThat]
biodb.TRACE[2024-10-14 01:33:13.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:13.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:13.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:13.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:13.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:13.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:13.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:13.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:13.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:13.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:13.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:13.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:33:13.528][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-14 01:33:13.537][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-14 01:33:13.540][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-14 01:33:13.543][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-14 01:33:13.546][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-10-14 01:33:13.714][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-10-14 01:33:13.724][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-14 01:33:13.728][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-10-14 01:33:13.733][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-14 01:33:13.741][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-10-14 01:33:13.777][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-14 01:33:13.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-14 01:33:13.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:13.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:13.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-14 01:33:13.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-14 01:33:13.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:13.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:13.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:13.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:13.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:13.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:14.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:14.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:14.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:14.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:14.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:14.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:14.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:14.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:14.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:14.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:14.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:14.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:14.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:14.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:14.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:14.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:33:14.069][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-10-14 01:33:14.152][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:33:14.169][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:33:14.283][private$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[2024-10-14 01:33:14.802][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-10-14 01:33:21.076][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:33:21.086][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-10-14 01:33:21.443][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-10-14 01:33:25.569][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[2024-10-14 01:33:25.578][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:33:25.580][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:33:25.589][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-10-14 01:33:25.963][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-10-14 01:33:26.328][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:33:26.333][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-10-14 01:33:26.343][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-10-14 01:33:26.393][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-10-14 01:33:26.402][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:33:26.405][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:33:26.408][rule$waitAsNeeded] Wait 0.175377 second(s).
biodb.TRACE[2024-10-14 01:33:26.589][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-10-14 01:33:26.969][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-10-14 01:33:27.334][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:33:27.339][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-10-14 01:33:27.349][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-10-14 01:33:27.389][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-14 01:33:27.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-14 01:33:27.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:27.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-14 01:33:27.435][biodb::testThat]
biodb.INFO [2024-10-14 01:33:27.438][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-10-14 01:33:27.440][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:27.442][biodb::testThat]
biodb.TRACE[2024-10-14 01:33:27.449][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-14 01:33:27.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-14 01:33:27.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:27.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:27.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-14 01:33:27.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-14 01:33:27.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:27.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:27.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:27.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:27.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:27.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:27.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:27.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:27.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:27.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:27.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:27.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:27.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:27.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:27.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:27.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:27.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:27.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:33:27.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:27.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:27.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:27.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:27.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:27.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:27.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:27.671][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-10-14 01:33:27.697][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:33:27.700][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:33:27.720][private$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[2024-10-14 01:33:28.317][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-10-14 01:33:33.281][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:33:33.290][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-10-14 01:33:33.731][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-10-14 01:33:37.995][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-10-14 01:33:38.340][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-14 01:33:38.372][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-10-14 01:33:38.376][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-10-14 01:33:38.379][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-14 01:33:38.388][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-14 01:33:38.391][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-14 01:33:38.399][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-14 01:33:38.407][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-14 01:33:38.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:38.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:38.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:38.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:38.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:38.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:38.532][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[2024-10-14 01:33:38.534][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-10-14 01:33:38.546][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:33:38.548][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:33:38.551][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-10-14 01:33:38.904][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-10-14 01:33:39.260][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:33:39.265][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-10-14 01:33:39.273][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-10-14 01:33:39.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:39.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:39.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:39.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:39.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:39.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:39.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:39.301][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-10-14 01:33:39.308][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:33:39.310][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:33:39.313][rule$waitAsNeeded] Wait 0.238553 second(s).
biodb.TRACE[2024-10-14 01:33:39.555][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-10-14 01:33:39.885][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-10-14 01:33:40.218][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:33:40.223][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-10-14 01:33:40.231][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-10-14 01:33:40.237][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-10-14 01:33:40.241][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-14 01:33:40.244][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-14 01:33:40.247][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-14 01:33:40.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:40.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:40.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:40.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:40.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:40.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:40.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:33:40.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:40.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:40.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:40.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:40.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:33:40.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:33:40.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:33:40.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:33:40.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.390][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:33:40.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:33:40.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.430][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:33:40.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:33:40.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.452][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:40.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:40.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.464][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:40.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:40.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.487][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:40.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:40.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.525][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:40.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:40.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.550][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:33:40.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:40.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.580][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:33:40.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:40.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.624][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:40.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:40.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:40.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:40.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:40.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:40.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:40.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:40.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.787][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:33:40.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:40.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.825][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-14 01:33:40.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:40.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:40.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:40.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.877][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:40.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:40.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.892][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:33:40.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:40.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.907][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:40.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:40.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:40.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:40.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:40.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:40.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:40.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:40.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.021][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:41.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:41.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:41.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:41.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:41.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:41.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:41.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:41.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:33:41.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:41.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:41.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:41.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:41.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:41.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:41.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:33:41.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:41.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:41.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:41.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:41.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:33:41.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:33:41.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.363][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:33:41.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:33:41.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.389][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:33:41.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:33:41.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.437][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:41.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:41.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.519][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:41.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:33:41.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.568][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:41.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:41.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.593][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:41.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:33:41.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.615][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:33:41.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:41.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.638][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:33:41.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:41.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.659][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:41.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:41.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.682][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:33:41.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:33:41.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:41.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:41.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:41.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:41.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.772][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:33:41.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:41.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.796][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-14 01:33:41.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:41.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:41.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:41.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:33:41.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:41.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.878][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:33:41.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:33:41.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.910][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:41.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:41.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.935][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:41.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:41.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:41.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:41.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:41.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:41.991][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:41.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:42.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:42.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:42.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:42.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:42.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:42.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:42.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:42.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:42.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:42.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:42.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:42.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:42.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:42.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:42.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:42.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:33:42.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:33:42.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:33:42.283][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-10-14 01:33:42.353][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-14 01:33:42.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:42.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:42.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:42.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:42.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:42.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:42.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:33:42.427][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.462][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.486][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:42.499][private$selectFields]
biodb.TRACE[2024-10-14 01:33:42.505][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-14 01:33:42.509][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-14 01:33:42.538][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:42.541][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.544][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.550][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.554][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.561][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.567][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.579][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:42.582][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:42.585][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.598][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.604][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.616][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-14 01:33:42.622][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.657][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.684][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.763][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-14 01:33:42.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:42.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:42.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:42.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:42.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:42.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:42.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:33:42.795][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.855][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.883][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:42.901][private$selectFields]
biodb.TRACE[2024-10-14 01:33:42.903][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-14 01:33:42.905][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-14 01:33:42.908][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:42.920][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.923][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.929][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.931][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.934][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.956][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.960][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:42.962][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:42.965][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.967][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:42.978][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:42.980][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-14 01:33:42.983][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:42.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.030][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.059][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.069][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-14 01:33:43.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:43.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:43.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:43.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:43.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:43.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:43.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:33:43.130][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.154][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.174][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:43.177][private$selectFields]
biodb.TRACE[2024-10-14 01:33:43.180][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-14 01:33:43.182][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-14 01:33:43.208][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:43.223][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.225][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.230][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.236][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.238][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.243][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.245][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:43.266][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:43.288][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.298][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.303][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.305][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-14 01:33:43.309][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.343][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.371][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:43.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.394][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-14 01:33:43.397][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-14 01:33:43.399][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-14 01:33:43.458][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-14 01:33:43.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-14 01:33:43.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-14 01:33:43.515][biodb::testThat]
biodb.INFO [2024-10-14 01:33:43.527][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-10-14 01:33:43.531][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:43.546][biodb::testThat]
biodb.TRACE[2024-10-14 01:33:43.788][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-14 01:33:43.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-14 01:33:43.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-14 01:33:43.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-14 01:33:43.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:43.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:43.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:43.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:43.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:43.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:43.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:43.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:43.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:43.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:43.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:33:44.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:44.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:44.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:44.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:44.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:44.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:44.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:44.309][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-10-14 01:33:44.323][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:33:44.325][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:33:44.331][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-10-14 01:33:44.841][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-10-14 01:33:50.648][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:33:50.653][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-10-14 01:33:50.923][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-10-14 01:33:57.799][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-14 01:33:57.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:57.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:57.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:57.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:57.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:57.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:57.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:33:57.953][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:57.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:57.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:57.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:57.970][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:57.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:57.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:57.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.041][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:58.043][private$selectFields]
biodb.TRACE[2024-10-14 01:33:58.046][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-14 01:33:58.048][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-14 01:33:58.051][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:58.053][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.056][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.061][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.064][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.066][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.071][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.073][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:58.111][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:58.114][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.116][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.121][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.124][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-14 01:33:58.126][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.136][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.145][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.159][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-14 01:33:58.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:58.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:58.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:58.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:58.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:58.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:58.188][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.TRACE[2024-10-14 01:33:58.191][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.202][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.214][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:58.216][private$selectFields]
biodb.TRACE[2024-10-14 01:33:58.219][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-14 01:33:58.222][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-14 01:33:58.224][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:58.227][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.229][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.234][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.236][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.239][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.244][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.247][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:58.250][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:58.253][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.256][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.263][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.266][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-14 01:33:58.269][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.282][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.306][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.316][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-14 01:33:58.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:58.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:58.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:58.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:58.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:58.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:58.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:33:58.364][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.375][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.387][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:58.390][private$selectFields]
biodb.TRACE[2024-10-14 01:33:58.393][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-14 01:33:58.398][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-14 01:33:58.401][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:58.405][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.408][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.414][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.420][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.423][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.430][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.433][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:58.436][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:33:58.438][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.441][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.446][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.448][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-14 01:33:58.453][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.464][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.480][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:33:58.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.495][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-14 01:33:58.497][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-14 01:33:58.501][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-14 01:33:58.537][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-14 01:33:58.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-14 01:33:58.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-14 01:33:58.571][biodb::testThat]
biodb.INFO [2024-10-14 01:33:58.573][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-10-14 01:33:58.576][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:33:58.579][biodb::testThat]
biodb.TRACE[2024-10-14 01:33:58.599][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-14 01:33:58.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-14 01:33:58.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-14 01:33:58.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-14 01:33:58.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:58.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:58.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:58.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:58.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:58.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:58.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:33:58.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:58.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:33:58.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:33:58.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:33:58.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:33:58.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:33:58.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:33:58.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:33:58.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:33:58.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:33:58.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:33:58.969][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-10-14 01:33:58.980][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-14 01:33:58.983][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-10-14 01:33:58.986][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-14 01:33:59.051][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-10-14 01:34:01.494][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-14 01:34:01.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:01.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:01.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:01.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:01.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:01.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:01.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:34:01.540][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.549][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.567][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:01.569][private$selectFields]
biodb.TRACE[2024-10-14 01:34:01.574][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-14 01:34:01.576][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-14 01:34:01.578][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:01.580][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.582][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.585][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.586][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.587][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.590][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.591][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:01.593][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:01.594][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.595][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.598][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.601][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-14 01:34:01.603][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.613][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.624][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.635][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-10-14 01:34:01.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:01.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:01.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:01.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:01.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:01.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:01.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:34:01.665][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.676][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.686][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:01.688][private$selectFields]
biodb.TRACE[2024-10-14 01:34:01.691][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-14 01:34:01.694][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-14 01:34:01.696][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:01.699][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.702][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.707][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.709][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.712][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.716][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.719][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:01.721][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:01.724][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.726][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.732][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.734][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-14 01:34:01.737][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.748][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.780][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.794][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-10-14 01:34:01.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:01.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:01.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:01.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:01.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:01.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:01.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:34:01.823][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.832][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.841][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:01.843][private$selectFields]
biodb.TRACE[2024-10-14 01:34:01.844][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-14 01:34:01.846][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-14 01:34:01.847][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:01.849][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.852][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.856][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.858][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.861][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.873][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.875][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:01.883][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:01.885][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.888][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.895][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.896][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-10-14 01:34:01.898][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.907][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.918][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:01.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:01.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:01.931][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-10-14 01:34:01.934][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-14 01:34:01.936][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-14 01:34:01.992][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-14 01:34:01.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-14 01:34:01.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:02.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-14 01:34:02.011][biodb::testThat]
biodb.INFO [2024-10-14 01:34:02.013][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-10-14 01:34:02.016][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:34:02.018][biodb::testThat]
biodb.DEBUG[2024-10-14 01:34:02.022][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-10-14 01:34:02.025][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-14 01:34:02.030][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-10-14 01:34:02.079][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-14 01:34:02.082][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-14 01:34:02.086][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-14 01:34:02.088][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-14 01:34:02.091][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-14 01:34:02.094][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-14 01:34:02.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:02.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:02.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:02.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:02.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:02.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:02.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:02.165][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-10-14 01:34:02.173][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:02.176][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:34:02.181][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-14 01:34:02.514][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:02.540][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:02.543][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-14 01:34:02.548][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-14 01:34:03.103][private$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[2024-10-14 01:34:03.126][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:03.146][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:03.150][rule$waitAsNeeded] Wait 0.0295191 second(s).
biodb.TRACE[2024-10-14 01:34:03.272][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-14 01:34:03.606][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:03.608][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:03.611][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[2024-10-14 01:34:03.615][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-14 01:34:04.149][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-14 01:34:04.165][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:04.168][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:04.171][rule$waitAsNeeded] Wait 0.0986249 second(s).
biodb.TRACE[2024-10-14 01:34:04.275][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-14 01:34:04.607][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:04.609][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:04.612][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-14 01:34:04.615][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-14 01:34:05.384][private$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[2024-10-14 01:34:05.387][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:05.389][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:34:05.392][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-14 01:34:05.721][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:05.723][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:05.724][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-14 01:34:05.725][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-14 01:34:06.279][private$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[2024-10-14 01:34:06.281][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:06.283][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:06.285][rule$waitAsNeeded] Wait 0.106959 second(s).
biodb.TRACE[2024-10-14 01:34:06.525][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-14 01:34:06.853][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:06.855][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:06.869][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[2024-10-14 01:34:06.872][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-14 01:34:07.203][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-14 01:34:07.206][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:07.209][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:07.212][rule$waitAsNeeded] Wait 0.312409 second(s).
biodb.TRACE[2024-10-14 01:34:07.664][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-14 01:34:07.994][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:07.996][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:07.998][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-14 01:34:08.001][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-14 01:34:08.788][private$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[2024-10-14 01:34:08.794][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:08.796][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:34:08.799][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-14 01:34:09.128][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:09.131][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:09.133][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-14 01:34:09.136][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-14 01:34:09.479][private$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[2024-10-14 01:34:09.481][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:09.485][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:09.488][rule$waitAsNeeded] Wait 0.311379 second(s).
biodb.TRACE[2024-10-14 01:34:09.913][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-14 01:34:10.413][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:10.415][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:10.418][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[2024-10-14 01:34:10.420][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-14 01:34:10.968][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-14 01:34:10.970][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:10.971][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:34:10.974][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-14 01:34:11.306][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:11.310][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:11.342][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[2024-10-14 01:34:11.385][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-14 01:34:11.963][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-14 01:34:11.966][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:11.968][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:11.974][rule$waitAsNeeded] Wait 0.00296998 second(s).
biodb.TRACE[2024-10-14 01:34:11.993][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-10-14 01:34:12.326][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:12.328][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:12.330][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-14 01:34:12.333][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-10-14 01:34:13.007][private$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[2024-10-14 01:34:13.012][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-10-14 01:34:13.017][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-14 01:34:13.020][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-10-14 01:34:13.024][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-14 01:34:13.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:13.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:13.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:13.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:13.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:13.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:13.057][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.TRACE[2024-10-14 01:34:13.061][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:13.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:13.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:13.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:13.072][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:13.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:13.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:13.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:13.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:13.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:13.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:13.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:13.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:13.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:13.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:13.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:13.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:13.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:13.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:13.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:13.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:13.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:13.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:13.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:13.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:13.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:13.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:13.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:13.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:13.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:13.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:13.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:34:13.165][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-10-14 01:34:13.168][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-10-14 01:34:13.193][biodb::testThat]
biodb.INFO [2024-10-14 01:34:13.195][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-10-14 01:34:13.198][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:34:13.200][biodb::testThat]
biodb.DEBUG[2024-10-14 01:34:13.226][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-10-14 01:34:13.233][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-10-14 01:34:13.236][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-14 01:34:13.240][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-10-14 01:34:13.245][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-10-14 01:34:13.248][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-14 01:34:13.251][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-14 01:34:13.253][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-14 01:34:13.256][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-14 01:34:13.259][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-14 01:34:13.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:13.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:13.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:13.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:13.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:13.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:13.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:13.301][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-10-14 01:34:13.308][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:13.312][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:34:13.316][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-14 01:34:13.646][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:13.653][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:13.658][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[2024-10-14 01:34:13.663][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-14 01:34:14.099][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-14 01:34:14.102][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:14.104][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:14.107][rule$waitAsNeeded] Wait 0.208332 second(s).
biodb.TRACE[2024-10-14 01:34:14.456][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-14 01:34:14.817][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:14.820][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:14.822][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-14 01:34:14.825][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-14 01:34:15.292][private$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[2024-10-14 01:34:15.337][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:15.340][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:15.342][rule$waitAsNeeded] Wait 0.112664 second(s).
biodb.TRACE[2024-10-14 01:34:15.459][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-14 01:34:15.787][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:15.789][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:15.792][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[2024-10-14 01:34:15.794][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-14 01:34:16.345][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-14 01:34:16.347][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:16.350][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:16.353][rule$waitAsNeeded] Wait 0.106126 second(s).
biodb.TRACE[2024-10-14 01:34:16.501][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-14 01:34:16.829][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:16.831][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:16.834][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-14 01:34:16.837][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-14 01:34:17.266][private$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[2024-10-14 01:34:17.291][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:17.294][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:17.296][rule$waitAsNeeded] Wait 0.204183 second(s).
biodb.TRACE[2024-10-14 01:34:17.504][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-14 01:34:17.836][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:17.872][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:17.876][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[2024-10-14 01:34:17.879][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-14 01:34:18.609][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-14 01:34:18.617][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:18.633][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:34:18.638][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-14 01:34:18.972][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:18.977][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:18.981][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[2024-10-14 01:34:18.984][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-14 01:34:19.618][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-14 01:34:19.654][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:19.656][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:34:19.660][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-14 01:34:19.989][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:20.006][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:20.009][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[2024-10-14 01:34:20.012][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-14 01:34:20.461][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-14 01:34:20.463][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:20.466][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:20.468][rule$waitAsNeeded] Wait 0.191255 second(s).
biodb.TRACE[2024-10-14 01:34:20.770][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-14 01:34:21.099][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:21.101][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:21.104][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-14 01:34:21.108][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-14 01:34:21.670][private$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[2024-10-14 01:34:21.672][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:21.675][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:21.678][rule$waitAsNeeded] Wait 0.0911889 second(s).
biodb.TRACE[2024-10-14 01:34:21.815][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-14 01:34:22.148][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:22.151][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:22.154][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[2024-10-14 01:34:22.157][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-14 01:34:22.678][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-10-14 01:34:22.680][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:22.681][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:22.682][rule$waitAsNeeded] Wait 0.131264 second(s).
biodb.TRACE[2024-10-14 01:34:22.958][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-10-14 01:34:23.284][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-10-14 01:34:23.287][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-10-14 01:34:23.289][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-10-14 01:34:23.292][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-10-14 01:34:23.918][private$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[2024-10-14 01:34:23.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:23.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:23.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:23.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:23.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:23.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:23.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:23.959][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-10-14 01:34:23.983][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:23.986][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:34:23.989][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-10-14 01:34:24.321][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2024-10-14 01:34:24.656][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:34:24.662][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2024-10-14 01:34:24.671][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2024-10-14 01:34:24.679][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-10-14 01:34:24.683][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-14 01:34:24.687][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-14 01:34:24.689][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-14 01:34:24.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:24.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:24.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:24.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:24.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:24.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:24.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:34:24.737][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:24.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:24.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:24.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:24.749][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:24.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:24.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:24.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:24.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:24.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:24.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:24.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:34:24.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:24.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:24.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:24.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:24.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:24.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:24.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:34:24.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:24.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:24.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:24.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:24.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:24.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:24.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:24.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:24.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:24.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:24.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:24.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:24.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:24.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:24.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:24.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:24.894][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:34:24.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:34:24.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:24.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:24.904][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:34:24.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:34:24.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:24.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:24.914][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:34:24.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:34:24.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:24.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:24.924][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:34:24.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:34:24.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:24.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:24.934][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:24.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:24.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:24.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.004][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:25.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:25.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.015][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:25.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:25.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.026][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:25.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:25.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.037][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:34:25.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:25.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.049][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:34:25.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:25.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.060][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:25.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:25.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.070][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:25.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:25.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.082][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:25.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:25.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:25.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:25.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.104][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:34:25.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:25.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.171][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-14 01:34:25.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:25.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.181][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:25.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:25.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:25.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:25.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.200][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:34:25.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:25.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.210][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:25.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:25.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.221][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:25.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:25.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:25.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:25.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.249][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:25.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:25.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:25.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:25.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.268][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:25.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:25.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.279][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:25.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:25.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:25.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:25.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.298][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:25.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:25.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:25.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:25.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:25.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:25.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:25.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:25.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:25.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:25.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:25.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:25.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:25.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:25.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:25.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:25.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:25.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:25.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:25.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:25.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:25.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:25.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:25.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:25.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:25.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:25.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:34:25.404][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2024-10-14 01:34:25.407][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-10-14 01:34:25.411][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-10-14 01:34:25.481][biodb::testThat]
biodb.INFO [2024-10-14 01:34:25.483][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-10-14 01:34:25.485][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:34:25.488][biodb::testThat]
biodb.INFO [2024-10-14 01:34:25.552][biodb::testThat]
biodb.INFO [2024-10-14 01:34:25.555][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-10-14 01:34:25.558][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:34:25.566][biodb::testThat]
biodb.INFO [2024-10-14 01:34:25.585][biodb::testThat]
biodb.INFO [2024-10-14 01:34:25.589][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-10-14 01:34:25.591][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:34:25.593][biodb::testThat]
biodb.DEBUG[2024-10-14 01:34:25.602][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-10-14 01:34:25.611][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:25.614][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:34:25.618][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-10-14 01:34:26.121][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-10-14 01:34:29.615][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:34:29.621][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-10-14 01:34:29.927][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-10-14 01:34:32.230][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:32.238][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:32.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:32.243][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:32.248][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:32.251][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:32.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:32.257][ef$get] fields variable is a list.
biodb.INFO [2024-10-14 01:34:32.265][biodb::testThat]
biodb.INFO [2024-10-14 01:34:32.267][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-10-14 01:34:32.270][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:34:32.272][biodb::testThat]
biodb.ERROR[2024-10-14 01:34:32.301][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-10-14 01:34:32.362][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-10-14 01:34:32.411][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-14 01:34:32.414][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-14 01:34:32.422][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-14 01:34:32.425][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-14 01:34:32.427][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:32.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:32.431][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:32.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:32.435][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.437][FUN] Functions in observer BiodbConfig: [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 [2024-10-14 01:34:32.474][biodb::testContext]
biodb.INFO [2024-10-14 01:34:32.480][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-14 01:34:32.482][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-10-14 01:34:32.484][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-14 01:34:32.487][biodb::testContext]
biodb.INFO [2024-10-14 01:34:32.495][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-14 01:34:32.501][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-14 01:34:32.517][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-14 01:34:32.519][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-14 01:34:32.521][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-14 01:34:32.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.529][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-14 01:34:32.532][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-14 01:34:32.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.538][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[2024-10-14 01:34:32.541][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-14 01:34:32.545][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-14 01:34:32.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.557][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-14 01:34:32.561][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-14 01:34:32.563][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-14 01:34:32.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.571][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-14 01:34:32.573][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-14 01:34:32.575][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-14 01:34:32.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.601][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-14 01:34:32.604][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-14 01:34:32.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.648][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-14 01:34:32.650][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-14 01:34:32.653][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-14 01:34:32.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.661][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-14 01:34:32.664][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-14 01:34:32.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.672][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-14 01:34:32.676][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-14 01:34:32.678][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-14 01:34:32.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.716][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-14 01:34:32.719][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-14 01:34:32.721][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-14 01:34:32.723][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-14 01:34:32.727][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-14 01:34:32.729][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-14 01:34:32.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.738][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-14 01:34:32.742][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-14 01:34:32.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.751][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-14 01:34:32.755][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-14 01:34:32.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.763][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-14 01:34:32.766][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-14 01:34:32.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.776][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-14 01:34:32.779][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-14 01:34:32.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.785][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-14 01:34:32.787][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-14 01:34:32.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.796][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-14 01:34:32.798][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-14 01:34:32.867][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-14 01:34:32.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.876][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-14 01:34:32.881][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-14 01:34:32.884][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-14 01:34:32.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:32.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:32.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:32.894][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-14 01:34:32.898][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:32.901][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-14 01:34:32.903][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:32.904][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:34:32.907][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:32.909][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:34:32.912][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:32.914][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:34:32.918][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-14 01:34:32.920][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:34:32.923][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:32.925][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-14 01:34:32.928][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:34:32.931][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:32.933][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:32.935][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-14 01:34:32.935][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-14 01:34:32.935][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-14 01:34:32.935][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-14 01:34:32.935][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-14 01:34:32.937][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:34:32.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:32.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:32.948][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:34:32.950][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:32.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:32.956][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:34:32.959][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:32.961][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:34:32.963][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:34:32.966][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:32.971][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:32.974][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-14 01:34:32.979][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:32.983][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-14 01:34:32.986][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:32.988][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:34:32.991][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:32.994][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:34:32.996][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:32.999][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:34:33.001][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-14 01:34:33.005][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:34:33.007][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:33.010][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-14 01:34:33.013][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:34:33.016][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:33.018][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:33.020][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-14 01:34:33.020][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-14 01:34:33.020][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-14 01:34:33.020][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-14 01:34:33.020][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-14 01:34:33.023][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:34:33.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:33.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:33.029][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:34:33.031][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:33.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:33.035][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:34:33.043][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:33.048][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:34:33.050][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:34:33.052][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:33.057][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:33.061][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-14 01:34:33.066][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:33.068][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-14 01:34:33.071][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:33.073][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:34:33.076][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:33.078][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:34:33.080][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:33.083][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:34:33.098][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-14 01:34:33.101][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:34:33.103][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:33.106][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-14 01:34:33.109][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:34:33.112][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:33.114][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:33.116][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:33.119][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:34:33.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:33.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:33.128][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:34:33.131][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:33.134][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:33.137][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:34:33.140][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:33.143][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:34:33.145][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:34:33.147][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:33.149][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:33.162][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-14 01:34:33.168][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:33.171][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-14 01:34:33.174][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:33.176][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:34:33.179][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:33.181][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:34:33.183][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:33.185][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:34:33.186][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-14 01:34:33.188][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:34:33.191][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:33.194][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-14 01:34:33.196][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:34:33.199][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:33.203][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:33.206][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:33.209][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:34:33.211][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:33.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:33.216][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:34:33.219][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:33.222][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:33.225][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:34:33.228][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:33.230][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:34:33.233][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:34:33.236][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:33.239][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:33.242][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-14 01:34:33.244][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.488][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-14 01:34:33.492][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-14 01:34:33.496][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-14 01:34:33.500][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-14 01:34:33.519][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-14 01:34:33.523][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-14 01:34:33.526][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-14 01:34:33.530][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-14 01:34:33.533][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-14 01:34:33.538][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-14 01:34:33.543][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-14 01:34:33.547][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-14 01:34:33.551][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-14 01:34:33.555][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-14 01:34:33.559][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-14 01:34:33.563][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-14 01:34:33.567][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-14 01:34:33.570][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-14 01:34:33.576][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-14 01:34:33.579][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-14 01:34:33.583][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-14 01:34:33.587][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-14 01:34:33.591][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-14 01:34:33.594][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-14 01:34:33.598][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-14 01:34:33.603][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-14 01:34:33.606][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-14 01:34:33.610][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-14 01:34:33.613][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-14 01:34:33.617][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-14 01:34:33.623][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-14 01:34:33.627][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-14 01:34:33.631][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-14 01:34:33.634][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-14 01:34:33.637][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-14 01:34:33.640][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-14 01:34:33.643][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-14 01:34:33.649][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-14 01:34:33.653][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-14 01:34:33.657][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-14 01:34:33.662][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-14 01:34:33.668][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-14 01:34:33.673][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-14 01:34:33.677][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-14 01:34:33.681][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-14 01:34:33.689][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-14 01:34:33.693][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-14 01:34:33.698][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-14 01:34:33.704][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-14 01:34:33.708][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-14 01:34:33.712][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-14 01:34:33.717][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-14 01:34:33.721][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-14 01:34:33.741][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-14 01:34:33.745][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-14 01:34:33.748][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-14 01:34:33.753][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-14 01:34:33.756][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-14 01:34:33.760][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-14 01:34:33.764][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-14 01:34:33.767][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-14 01:34:33.770][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-14 01:34:33.774][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-14 01:34:33.778][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-14 01:34:33.787][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-14 01:34:33.791][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-14 01:34:33.795][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-14 01:34:33.799][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-14 01:34:33.802][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-14 01:34:33.809][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-14 01:34:33.814][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-14 01:34:33.819][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-14 01:34:33.828][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-14 01:34:33.833][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-14 01:34:33.842][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-14 01:34:33.846][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-14 01:34:33.850][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-14 01:34:33.855][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-14 01:34:33.858][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-14 01:34:33.861][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-14 01:34:33.865][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-14 01:34:33.868][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-14 01:34:33.871][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-14 01:34:33.879][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-14 01:34:33.888][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-14 01:34:33.891][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-14 01:34:33.894][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.898][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:33.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:33.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:33.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:33.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:33.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:33.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:33.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:33.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:33.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:33.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:33.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:33.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:33.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:34.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:34.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.075][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[2024-10-14 01:34:34.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.096][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[2024-10-14 01:34:34.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.114][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[2024-10-14 01:34:34.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:34.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.149][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[2024-10-14 01:34:34.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:34.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:34.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.218][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[2024-10-14 01:34:34.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.235][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[2024-10-14 01:34:34.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:34.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.294][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[2024-10-14 01:34:34.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:34.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:34.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:34.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:34.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:34.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:34.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:34.325][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-14 01:34:34.328][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-14 01:34:34.333][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:34.338][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-14 01:34:34.340][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:34.344][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:34:34.347][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:34.349][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:34:34.351][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:34.354][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:34:34.364][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-14 01:34:34.366][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:34:34.369][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:34.372][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-14 01:34:34.374][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:34:34.377][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-14 01:34:34.377][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-14 01:34:34.377][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-14 01:34:34.377][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-14 01:34:34.377][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-14 01:34:34.377][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-14 01:34:34.377][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-14 01:34:34.377][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-14 01:34:34.377][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-14 01:34:34.380][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:34.384][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-14 01:34:34.384][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-14 01:34:34.388][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:34:34.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:34.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:34.396][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:34:34.398][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:34.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:34.403][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:34:34.407][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-14 01:34:34.407][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-14 01:34:34.410][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:34:34.412][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:34:34.415][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:34.419][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:34.423][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-14 01:34:34.426][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-14 01:34:34.438][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-14 01:34:34.459][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-14 01:34:34.462][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-14 01:34:34.465][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-14 01:34:34.470][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-14 01:34:34.471][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-14 01:34:34.473][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-14 01:34:34.475][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-14 01:34:34.477][biodb::testThat]
biodb.INFO [2024-10-14 01:34:34.478][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-10-14 01:34:34.480][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:34:34.482][biodb::testThat]
biodb.DEBUG[2024-10-14 01:34:34.490][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[2024-10-14 01:34:34.512][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:34.514][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:34:34.518][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-10-14 01:34:34.883][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-10-14 01:34:35.254][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:34:35.258][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-10-14 01:34:35.271][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-10-14 01:34:35.293][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-10-14 01:34:35.303][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:35.305][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:35.307][rule$waitAsNeeded] Wait 0.209368 second(s).
biodb.TRACE[2024-10-14 01:34:35.524][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-10-14 01:34:35.893][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-10-14 01:34:36.257][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:34:36.262][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-10-14 01:34:36.273][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-10-14 01:34:36.306][biodb::testThat]
biodb.INFO [2024-10-14 01:34:36.308][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-10-14 01:34:36.311][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:34:36.313][biodb::testThat]
biodb.INFO [2024-10-14 01:34:36.378][biodb::testThat]
biodb.INFO [2024-10-14 01:34:36.380][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-10-14 01:34:36.383][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:34:36.385][biodb::testThat]
biodb.DEBUG[2024-10-14 01:34:36.393][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-10-14 01:34:36.401][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:36.404][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:36.407][rule$waitAsNeeded] Wait 0.115374 second(s).
biodb.TRACE[2024-10-14 01:34:36.526][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-10-14 01:34:36.849][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-10-14 01:34:37.171][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:34:37.177][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-10-14 01:34:37.195][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-10-14 01:34:37.209][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-10-14 01:34:37.221][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-14 01:34:37.224][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-10-14 01:34:37.227][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-14 01:34:37.232][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-10-14 01:34:37.246][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-10-14 01:34:37.255][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:37.257][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:37.260][rule$waitAsNeeded] Wait 0.265659 second(s).
biodb.TRACE[2024-10-14 01:34:37.530][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-10-14 01:34:37.857][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-10-14 01:34:38.180][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:34:38.197][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-10-14 01:34:38.207][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-10-14 01:34:38.225][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-10-14 01:34:38.233][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:38.236][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-14 01:34:38.239][rule$waitAsNeeded] Wait 0.289491 second(s).
biodb.TRACE[2024-10-14 01:34:38.648][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-10-14 01:34:39.182][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-10-14 01:34:40.552][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:34:40.572][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-10-14 01:34:40.730][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-10-14 01:34:41.037][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-10-14 01:34:41.091][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-14 01:34:41.104][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-14 01:34:41.109][private$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[2024-10-14 01:34:41.606][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-10-14 01:34:42.915][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-14 01:34:42.921][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-10-14 01:34:42.974][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-10-14 01:34:43.449][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-14 01:34:43.452][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-14 01:34:43.454][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-14 01:34:43.456][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-14 01:34:43.458][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:43.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:43.463][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:43.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:43.467][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.470][FUN] Functions in observer BiodbConfig: [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 [2024-10-14 01:34:43.480][biodb::testContext]
biodb.INFO [2024-10-14 01:34:43.483][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-14 01:34:43.485][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-10-14 01:34:43.489][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-14 01:34:43.503][biodb::testContext]
biodb.INFO [2024-10-14 01:34:43.508][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-14 01:34:43.513][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-14 01:34:43.528][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-14 01:34:43.530][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-14 01:34:43.534][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-14 01:34:43.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.543][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-14 01:34:43.546][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-14 01:34:43.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.553][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[2024-10-14 01:34:43.556][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-14 01:34:43.558][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-14 01:34:43.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.569][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-14 01:34:43.571][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-14 01:34:43.575][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-14 01:34:43.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.608][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-14 01:34:43.612][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-14 01:34:43.615][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-14 01:34:43.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.626][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-14 01:34:43.667][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-14 01:34:43.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.676][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-14 01:34:43.686][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-14 01:34:43.689][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-14 01:34:43.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.698][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-14 01:34:43.701][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-14 01:34:43.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.711][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-14 01:34:43.714][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-14 01:34:43.716][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-14 01:34:43.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.732][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-14 01:34:43.735][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-14 01:34:43.741][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-14 01:34:43.743][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-14 01:34:43.746][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-14 01:34:43.748][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-14 01:34:43.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.758][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-14 01:34:43.761][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-14 01:34:43.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.771][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-14 01:34:43.774][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-14 01:34:43.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.781][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[2024-10-14 01:34:43.783][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-14 01:34:43.786][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-14 01:34:43.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.796][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-14 01:34:43.799][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-14 01:34:43.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.810][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-14 01:34:43.813][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-14 01:34:43.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.823][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-14 01:34:43.826][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-14 01:34:43.848][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-14 01:34:43.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.858][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-14 01:34:43.878][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-14 01:34:43.929][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-14 01:34:43.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:43.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:43.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:43.938][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-14 01:34:43.943][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:43.945][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-14 01:34:43.948][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:43.951][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:34:43.953][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:43.956][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:34:43.958][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:43.961][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:34:43.965][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-14 01:34:43.968][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:34:43.976][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:43.985][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-14 01:34:43.988][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:34:43.991][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:43.993][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:43.996][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-14 01:34:43.996][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-14 01:34:43.996][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-14 01:34:43.996][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-14 01:34:43.996][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-14 01:34:43.999][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:34:44.002][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:44.005][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:44.007][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:34:44.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:44.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:44.015][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:34:44.018][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.021][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:34:44.023][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:34:44.027][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:44.030][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.033][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-14 01:34:44.040][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:44.043][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-14 01:34:44.046][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:44.048][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:34:44.051][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:44.054][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:34:44.056][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:44.059][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:34:44.062][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-14 01:34:44.065][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:34:44.067][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:44.070][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-14 01:34:44.073][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:34:44.075][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.078][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:44.080][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-14 01:34:44.080][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-14 01:34:44.080][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-14 01:34:44.080][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-14 01:34:44.080][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-14 01:34:44.083][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:34:44.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:44.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:44.150][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:34:44.154][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:44.156][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:44.158][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:34:44.161][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.163][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:34:44.166][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:34:44.168][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:44.171][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.174][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-14 01:34:44.179][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:44.188][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-14 01:34:44.198][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:44.206][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:34:44.209][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:44.212][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:34:44.215][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:44.218][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:34:44.220][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-14 01:34:44.223][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:34:44.225][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:44.228][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-14 01:34:44.230][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:34:44.232][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.235][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:44.237][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.240][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:34:44.242][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:44.244][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:44.247][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:34:44.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:44.251][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:44.254][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:34:44.256][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.258][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:34:44.260][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:34:44.263][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:44.265][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.268][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-14 01:34:44.273][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:44.275][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-14 01:34:44.278][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:44.281][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:34:44.283][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:44.286][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:34:44.289][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:44.291][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:34:44.294][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-14 01:34:44.296][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:34:44.299][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:44.301][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-14 01:34:44.303][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:34:44.306][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.309][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:44.311][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.314][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:34:44.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:44.335][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:44.338][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:34:44.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:44.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:44.384][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:34:44.386][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.389][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:34:44.392][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:34:44.394][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:44.397][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:44.400][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-14 01:34:44.403][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.483][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[2024-10-14 01:34:44.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.545][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[2024-10-14 01:34:44.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:44.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:44.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:44.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:44.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:44.710][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-14 01:34:44.714][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-14 01:34:44.718][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-14 01:34:44.721][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-14 01:34:44.725][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-14 01:34:44.729][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-14 01:34:44.732][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-14 01:34:44.736][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-14 01:34:44.739][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-14 01:34:44.743][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-14 01:34:44.748][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-14 01:34:44.752][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-14 01:34:44.755][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-14 01:34:44.760][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-14 01:34:44.764][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-14 01:34:44.768][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-14 01:34:44.772][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-14 01:34:44.786][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-14 01:34:44.825][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-14 01:34:44.829][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-14 01:34:44.832][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-14 01:34:44.842][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-14 01:34:44.846][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-14 01:34:44.851][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-14 01:34:44.855][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-14 01:34:44.858][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-14 01:34:44.862][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-14 01:34:44.866][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-14 01:34:44.869][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-14 01:34:44.874][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-14 01:34:44.877][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-14 01:34:44.882][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-14 01:34:44.886][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-14 01:34:44.889][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-14 01:34:44.893][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-14 01:34:44.896][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-14 01:34:44.900][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-14 01:34:44.906][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-14 01:34:44.909][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-14 01:34:44.912][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-14 01:34:44.936][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-14 01:34:44.940][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-14 01:34:44.943][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-14 01:34:44.947][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-14 01:34:44.952][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-14 01:34:44.956][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-14 01:34:44.959][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-14 01:34:44.964][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-14 01:34:44.967][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-14 01:34:44.971][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-14 01:34:44.974][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-14 01:34:44.978][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-14 01:34:44.982][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-14 01:34:44.985][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-14 01:34:44.989][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-14 01:34:44.992][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-14 01:34:44.997][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-14 01:34:45.002][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-14 01:34:45.006][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-14 01:34:45.010][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-14 01:34:45.014][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-14 01:34:45.017][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-14 01:34:45.035][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-14 01:34:45.039][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-14 01:34:45.042][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-14 01:34:45.085][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-14 01:34:45.089][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-14 01:34:45.092][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-14 01:34:45.096][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-14 01:34:45.100][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-14 01:34:45.104][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-14 01:34:45.108][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-14 01:34:45.112][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-14 01:34:45.115][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-14 01:34:45.119][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-14 01:34:45.123][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-14 01:34:45.127][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-14 01:34:45.131][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-14 01:34:45.134][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-14 01:34:45.142][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-14 01:34:45.146][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-14 01:34:45.149][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-14 01:34:45.155][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-14 01:34:45.159][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-14 01:34:45.165][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-14 01:34:45.168][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-14 01:34:45.170][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.176][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.212][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[2024-10-14 01:34:45.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.395][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[2024-10-14 01:34:45.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-14 01:34:45.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:45.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:45.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:45.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:45.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:45.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-14 01:34:45.496][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-10-14 01:34:45.499][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-10-14 01:34:45.504][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:45.507][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-14 01:34:45.510][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:45.512][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-14 01:34:45.515][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:45.518][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-14 01:34:45.520][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:45.523][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-14 01:34:45.526][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-14 01:34:45.550][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-14 01:34:45.552][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:45.555][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-10-14 01:34:45.558][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-14 01:34:45.560][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-10-14 01:34:45.560][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-10-14 01:34:45.560][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-10-14 01:34:45.560][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-10-14 01:34:45.560][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-10-14 01:34:45.560][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-10-14 01:34:45.560][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-10-14 01:34:45.560][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-10-14 01:34:45.560][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-10-14 01:34:45.563][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-14 01:34:45.566][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-14 01:34:45.566][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-14 01:34:45.569][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-14 01:34:45.572][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:45.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:45.576][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-14 01:34:45.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-14 01:34:45.581][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-14 01:34:45.583][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-14 01:34:45.586][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-10-14 01:34:45.586][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-10-14 01:34:45.589][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-14 01:34:45.592][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-14 01:34:45.595][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-14 01:34:45.597][self$setPropertyValue]
biodb.DEBUG[2024-10-14 01:34:45.601][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-10-14 01:34:45.605][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-14 01:34:45.614][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-10-14 01:34:45.616][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-10-14 01:34:45.620][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-10-14 01:34:45.623][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-10-14 01:34:45.626][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-14 01:34:45.630][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-10-14 01:34:45.634][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-10-14 01:34:45.658][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-10-14 01:34:45.663][biodb::testThat]
biodb.INFO [2024-10-14 01:34:45.666][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-10-14 01:34:45.672][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-14 01:34:45.675][biodb::testThat]
biodb.DEBUG[2024-10-14 01:34:45.684][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[2024-10-14 01:34:45.696][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-14 01:34:45.699][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-10-14 01:34:45.704][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-14 01:34:45.758][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-10-14 01:34:48.352][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-10-14 01:34:48.354][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-14 01:34:48.358][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-10-14 01:34:48.362][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-10-14 01:34:48.367][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-10-14 01:34:48.371][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-10-14 01:34:48.375][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-10-14 01:34:48.377][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-10-14 01:34:48.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:48.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:48.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:48.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:48.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:48.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:48.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:34:48.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:48.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:48.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:48.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:48.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:48.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:48.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:48.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:48.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.521][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:34:48.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:34:48.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.585][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:34:48.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:34:48.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.595][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:48.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:48.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.606][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:48.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:48.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.625][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:48.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:48.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.653][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:48.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:48.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.665][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:34:48.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:48.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.676][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:34:48.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:48.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.688][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:48.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:48.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.699][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:48.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:48.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:48.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:48.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:48.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:48.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.734][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:34:48.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:48.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.744][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-14 01:34:48.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:48.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:48.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:48.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:48.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:48.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.846][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:34:48.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:48.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:48.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:48.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:48.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:48.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.885][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:48.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:48.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:48.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:48.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:48.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:48.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.910][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:48.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:48.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.916][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:48.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:48.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:48.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:48.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.930][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:48.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:48.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:48.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:48.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:48.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:48.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:48.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:48.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:48.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:48.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:34:48.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:48.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:48.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:48.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:48.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:48.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:49.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:34:49.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:49.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:49.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:49.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:49.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.062][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:34:49.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-14 01:34:49.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.080][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:34:49.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-14 01:34:49.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.169][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:49.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:49.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.180][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:49.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:49.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.194][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:49.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:49.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.205][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:49.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:49.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.218][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:34:49.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:49.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.228][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-10-14 01:34:49.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:49.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:49.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:49.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.248][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:49.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:49.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:49.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:49.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:49.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:49.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.285][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:34:49.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:49.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.301][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-10-14 01:34:49.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:49.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:49.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:49.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:49.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:49.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.338][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-10-14 01:34:49.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:49.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.353][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:49.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:49.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.366][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:49.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:49.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.459][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:49.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:49.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-14 01:34:49.629][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-10-14 01:34:49.635][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-14 01:34:49.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:49.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:49.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:49.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:49.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:49.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:49.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:34:49.666][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-14 01:34:49.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-14 01:34:49.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.767][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-14 01:34:49.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-14 01:34:49.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.778][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-14 01:34:49.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-14 01:34:49.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.788][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-14 01:34:49.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-14 01:34:49.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.802][private$selectFields] Fields none
biodb.TRACE[2024-10-14 01:34:49.804][private$selectFields]
biodb.TRACE[2024-10-14 01:34:49.807][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-10-14 01:34:49.809][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-14 01:34:49.812][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:49.814][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.817][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.821][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.824][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:49.827][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:49.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.832][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.834][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:49.838][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:49.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.843][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.848][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:49.851][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:49.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.856][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.858][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:49.861][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:49.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.865][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.867][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:49.870][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:49.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.875][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.877][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:49.880][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:49.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.885][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.887][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:49.890][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:49.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.894][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.897][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:49.900][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:49.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.905][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.907][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:49.910][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:49.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.915][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.920][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:49.924][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:49.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.929][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.932][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:49.937][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:49.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.943][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.948][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:49.951][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:49.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.956][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.959][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:49.962][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:49.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.968][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.972][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:49.975][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:49.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.980][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.982][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:49.985][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:49.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:49.990][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:49.993][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:49.995][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:49.998][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:50.001][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:50.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.047][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.049][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.052][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.057][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.059][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.062][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.067][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.069][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.072][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.076][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.079][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.081][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.086][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.088][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:50.090][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:50.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.095][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.097][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:50.099][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:50.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.104][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.108][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.111][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.116][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.119][private$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[2024-10-14 01:34:50.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:50.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:50.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:50.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:50.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:50.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:50.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.195][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.205][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.216][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.227][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.237][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.248][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.292][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:50.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:50.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.302][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:50.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:50.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:50.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:50.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:50.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:50.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.348][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:50.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:50.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:50.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:50.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.365][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.375][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.385][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.411][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-10-14 01:34:50.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-14 01:34:50.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:50.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:50.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:50.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:50.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:50.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-14 01:34:50.449][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-14 01:34:50.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-14 01:34:50.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.461][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-14 01:34:50.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-14 01:34:50.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.472][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-14 01:34:50.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-14 01:34:50.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.482][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-14 01:34:50.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-14 01:34:50.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.493][private$selectFields] Fields none
biodb.TRACE[2024-10-14 01:34:50.496][private$selectFields]
biodb.TRACE[2024-10-14 01:34:50.499][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-10-14 01:34:50.502][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-14 01:34:50.505][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:50.507][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:50.510][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:50.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.515][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.518][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.526][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.548][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.550][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.553][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.557][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.559][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.561][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.565][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.567][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.569][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.574][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.576][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:50.578][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:50.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.583][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.585][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:50.590][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:50.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.614][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.616][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.619][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.623][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.626][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:50.628][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:50.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.633][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.635][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.644][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.646][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.649][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.654][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.658][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.661][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.669][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.671][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.676][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.680][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.683][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:50.685][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:50.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.689][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.690][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:50.692][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:50.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.695][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.696][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.698][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.702][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.704][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:50.709][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-10-14 01:34:50.712][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:50.715][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:50.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.720][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.722][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.725][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.729][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.732][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.734][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.736][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.738][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.741][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.743][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.748][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.750][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.753][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.757][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.760][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:50.762][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:50.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.767][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.770][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:50.776][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:50.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.781][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.785][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.788][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:50.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.808][ef$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.811][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-10-14 01:34:50.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:50.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:50.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:50.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:50.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-14 01:34:50.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-14 01:34:50.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-14 01:34:50.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.870][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.881][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.891][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-14 01:34:50.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.902][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.913][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.928][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-14 01:34:50.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-14 01:34:50.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.974][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:50.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:50.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:50.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:50.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:50.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:50.996][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-14 01:34:51.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-14 01:34:51.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:51.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:51.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:51.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:51.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:51.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:51.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:51.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:51.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:51.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:51.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-14 01:34:51.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-14 01:34:51.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:51.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:51.043][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:51.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:51.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:51.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:51.054][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:51.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:51.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:51.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:51.066][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:51.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-10-14 01:34:51.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-14 01:34:51.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-14 01:34:51.102][private$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[2024-10-14 01:34:51.104][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-10-14 01:34:51.106][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-10-14 01:34:51.137][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-14 01:34:51.140][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-10-14 01:34:51.143][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-10-14 01:34:51.145][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-14 01:34:51.147][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-14 01:34:51.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-14 01:34:51.151][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-14 01:34:51.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-14 01:34:51.155][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-14 01:34:51.157][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 168 ]
> 
> proc.time()
   user  system elapsed 
 39.681   5.127 121.620

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn 4.909 1.97919.061
LipidmapsStructureEntry0.6090.0331.067