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This page was generated on 2024-04-18 11:32:07 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 200/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_18
git_last_commit: f02eedd
git_last_commit_date: 2023-10-24 11:38:15 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for biodbLipidmaps on kjohnson1


To the developers/maintainers of the biodbLipidmaps package:
- 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: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2024-04-17 07:10:40 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 07:13:15 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 155.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/biodbLipidmaps.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
  any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  One of the entries is NULL.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
   3.   └─testthat::expect_false(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/biodbLipidmaps.Rcheck/00check.log’
for details.

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/4.3-arm64/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-04-17 07:11:31.325][biodb::testContext]
biodb.INFO [2024-04-17 07:11:31.331][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:11:31.332][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-04-17 07:11:31.333][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:11:31.334][biodb::testContext]
biodb.INFO [2024-04-17 07:11:31.345][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:11:31.347][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-17 07:11:31.359][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:11:31.360][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-17 07:11:31.361][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-17 07:11:31.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.365][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-17 07:11:31.385][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-17 07:11:31.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.389][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-17 07:11:31.390][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-17 07:11:31.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.394][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-17 07:11:31.395][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-17 07:11:31.396][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-17 07:11:31.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.400][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-17 07:11:31.401][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-17 07:11:31.401][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-17 07:11:31.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.405][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-17 07:11:31.406][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-17 07:11:31.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.409][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-17 07:11:31.410][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-17 07:11:31.411][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-17 07:11:31.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.414][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-17 07:11:31.415][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-17 07:11:31.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.417][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.DEBUG[2024-04-17 07:11:31.418][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-17 07:11:31.419][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-17 07:11:31.420][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-17 07:11:31.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.423][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:11:31.424][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-17 07:11:31.425][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-17 07:11:31.426][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-17 07:11:31.427][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-17 07:11:31.427][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-17 07:11:31.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.431][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-17 07:11:31.432][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-17 07:11:31.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.435][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-17 07:11:31.436][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-17 07:11:31.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.440][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-17 07:11:31.441][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-17 07:11:31.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.445][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-17 07:11:31.446][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-17 07:11:31.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.449][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-17 07:11:31.450][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-17 07:11:31.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.453][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:11:31.454][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-17 07:11:31.471][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-17 07:11:31.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.474][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[2024-04-17 07:11:31.475][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-17 07:11:31.476][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-17 07:11:31.477][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-17 07:11:31.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.485][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-17 07:11:31.525][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.542][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-17 07:11:31.543][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.544][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:11:31.545][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.546][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.547][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.548][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.549][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:11:31.550][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:11:31.551][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.552][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-17 07:11:31.553][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:11:31.554][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.554][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.555][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:11:31.555][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:11:31.555][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:11:31.555][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:11:31.555][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:11:31.556][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:11:31.557][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:11:31.558][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:11:31.559][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:11:31.560][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:11:31.561][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:11:31.562][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.562][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.571][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:11:31.572][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:11:31.573][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.574][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.575][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-17 07:11:31.577][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.578][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:11:31.578][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.579][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:11:31.580][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.581][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.582][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.583][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:11:31.584][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:11:31.585][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.585][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-17 07:11:31.586][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:11:31.587][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.588][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.589][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:11:31.589][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:11:31.589][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:11:31.589][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:11:31.589][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:11:31.589][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:11:31.590][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:11:31.591][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:11:31.592][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:11:31.593][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:11:31.593][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:11:31.594][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.595][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.596][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:11:31.596][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:11:31.597][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.598][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.599][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-17 07:11:31.601][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.602][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-17 07:11:31.603][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.603][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:11:31.604][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.605][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.606][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.607][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.608][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:11:31.608][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:11:31.609][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.610][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-17 07:11:31.611][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:11:31.612][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.612][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.613][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.614][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:11:31.615][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:11:31.615][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:11:31.616][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:11:31.617][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:11:31.618][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:11:31.618][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.619][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.620][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:11:31.621][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:11:31.621][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.622][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.623][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-17 07:11:31.625][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.626][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:11:31.627][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.627][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:11:31.628][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.629][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.630][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.631][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.631][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:11:31.632][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:11:31.633][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.634][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-17 07:11:31.634][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:11:31.635][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.636][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.637][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.638][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:11:31.638][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:11:31.639][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:11:31.640][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:11:31.641][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:11:31.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:11:31.642][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.643][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.644][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:11:31.644][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:11:31.645][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.646][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.652][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:11:31.653][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.685][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[2024-04-17 07:11:31.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.717][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-17 07:11:31.724][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-17 07:11:31.726][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-17 07:11:31.727][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-17 07:11:31.728][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-17 07:11:31.729][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-17 07:11:31.730][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-17 07:11:31.732][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-17 07:11:31.733][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-17 07:11:31.734][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-17 07:11:31.735][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-17 07:11:31.736][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-17 07:11:31.737][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-17 07:11:31.738][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-17 07:11:31.740][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-17 07:11:31.741][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-17 07:11:31.742][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-17 07:11:31.743][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-17 07:11:31.744][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-17 07:11:31.745][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-17 07:11:31.746][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-17 07:11:31.747][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-17 07:11:31.749][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-17 07:11:31.750][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-17 07:11:31.751][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-17 07:11:31.752][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-17 07:11:31.753][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-17 07:11:31.754][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-17 07:11:31.755][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-17 07:11:31.757][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-17 07:11:31.758][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-17 07:11:31.759][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-17 07:11:31.760][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-17 07:11:31.761][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-17 07:11:31.762][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-17 07:11:31.763][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-17 07:11:31.765][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-17 07:11:31.766][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-17 07:11:31.767][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-17 07:11:31.768][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-17 07:11:31.769][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-17 07:11:31.770][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-17 07:11:31.771][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-17 07:11:31.772][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-17 07:11:31.774][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-17 07:11:31.775][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-17 07:11:31.776][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-17 07:11:31.777][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-17 07:11:31.778][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-17 07:11:31.779][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-17 07:11:31.780][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-17 07:11:31.781][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-17 07:11:31.783][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-17 07:11:31.784][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-17 07:11:31.785][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-17 07:11:31.786][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-17 07:11:31.787][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-17 07:11:31.788][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-17 07:11:31.789][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-17 07:11:31.791][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-17 07:11:31.792][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-17 07:11:31.793][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-17 07:11:31.794][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-17 07:11:31.796][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-17 07:11:31.803][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-17 07:11:31.805][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-17 07:11:31.806][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-17 07:11:31.807][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-17 07:11:31.808][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-17 07:11:31.809][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-17 07:11:31.810][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-17 07:11:31.812][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-17 07:11:31.813][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-17 07:11:31.814][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-17 07:11:31.815][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-17 07:11:31.816][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-17 07:11:31.817][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-17 07:11:31.818][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-17 07:11:31.820][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-17 07:11:31.821][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-17 07:11:31.822][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-17 07:11:31.823][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-17 07:11:31.824][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-17 07:11:31.830][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-17 07:11:31.832][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:11:31.837][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:11:31.838][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.839][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.873][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[2024-04-17 07:11:31.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:11:31.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:31.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:31.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:31.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:31.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:31.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:31.927][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-04-17 07:11:31.937][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-04-17 07:11:31.939][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.940][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.941][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.941][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:11:31.942][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.943][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.944][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.945][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.945][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:11:31.946][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:11:31.947][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.948][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-04-17 07:11:31.949][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:11:31.949][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-04-17 07:11:31.949][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-04-17 07:11:31.949][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-04-17 07:11:31.949][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-04-17 07:11:31.949][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-04-17 07:11:31.949][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-04-17 07:11:31.949][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-04-17 07:11:31.949][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-04-17 07:11:31.949][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-04-17 07:11:31.950][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-17 07:11:31.951][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:11:31.951][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:11:31.952][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:11:31.953][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:11:31.953][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:11:31.954][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:11:31.955][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:11:31.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:11:31.956][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:11:31.957][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-17 07:11:31.957][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-04-17 07:11:31.958][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:11:31.959][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:11:31.959][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-17 07:11:31.960][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:11:31.966][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-04-17 07:11:31.967][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-17 07:11:32.006][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-04-17 07:11:32.008][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-04-17 07:11:32.014][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-04-17 07:11:32.021][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-04-17 07:11:32.027][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-17 07:11:32.028][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-17 07:11:32.029][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-04-17 07:11:32.030][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-04-17 07:11:32.045][biodb::testThat]
biodb.INFO [2024-04-17 07:11:32.046][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-04-17 07:11:32.047][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:11:32.048][biodb::testThat]
biodb.TRACE[2024-04-17 07:11:32.054][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-04-17 07:11:32.056][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:11:32.062][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-17 07:11:32.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:11:32.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:32.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:32.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:32.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:32.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:32.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:11:32.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:11:32.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:11:32.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.147][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-17 07:11:32.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-17 07:11:32.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.150][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:11:32.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:11:32.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.153][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.180][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.184][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.187][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.190][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-17 07:11:32.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.194][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-17 07:11:32.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.197][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:32.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:32.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.200][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:32.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:32.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.203][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.207][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.210][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-17 07:11:32.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.213][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-17 07:11:32.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.216][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.219][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.222][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-17 07:11:32.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.286][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.293][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.296][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.302][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:11:32.333][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-04-17 07:11:32.337][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:11:32.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:11:32.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.341][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:11:32.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:11:32.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.344][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-17 07:11:32.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-17 07:11:32.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.348][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-17 07:11:32.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-17 07:11:32.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.388][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.421][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.424][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.428][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.452][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.453][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.455][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.480][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.480][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.482][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.494][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.501][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.505][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.506][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.507][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.508][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.520][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:32.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:32.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.524][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:32.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:32.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.528][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:32.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:32.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.531][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:32.532][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:32.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.534][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.535][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:32.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:32.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.586][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.587][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.588][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.601][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.604][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.609][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.612][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.613][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.615][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.616][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.627][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.628][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.630][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.635][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.637][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.638][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.639][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.644][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:32.645][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:32.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.647][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.653][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.654][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.656][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.660][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.661][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.663][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.669][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.670][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.671][ef$get] fields variable is a list.
biodb.INFO [2024-04-17 07:11:32.680][biodb::testThat]
biodb.INFO [2024-04-17 07:11:32.681][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-04-17 07:11:32.682][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:11:32.682][biodb::testThat]
biodb.DEBUG[2024-04-17 07:11:32.695][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-04-17 07:11:32.707][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:11:32.712][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-04-17 07:11:32.713][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:11:32.714][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-04-17 07:11:32.715][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:11:32.738][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:11:32.740][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-17 07:11:32.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:11:32.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:32.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:32.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:32.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:32.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:32.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:11:32.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:11:32.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:11:32.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:11:32.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:11:32.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.773][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-17 07:11:32.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-17 07:11:32.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.776][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:11:32.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:11:32.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.779][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.783][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:32.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.787][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.790][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:32.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.794][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-17 07:11:32.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.797][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-17 07:11:32.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:32.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.801][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:32.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:32.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.806][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:32.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:32.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.824][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-17 07:11:32.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.827][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-17 07:11:32.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.837][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-17 07:11:32.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.844][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.853][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.857][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.860][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.867][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:32.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:32.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:32.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:11:32.893][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-04-17 07:11:32.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-17 07:11:32.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-17 07:11:32.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-17 07:11:32.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-17 07:11:32.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-17 07:11:32.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-17 07:11:32.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-17 07:11:32.912][biodb::testThat]
biodb.INFO [2024-04-17 07:11:32.913][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-04-17 07:11:32.914][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:11:32.915][biodb::testThat]
biodb.TRACE[2024-04-17 07:11:32.918][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.919][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.921][ef$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:11:32.922][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-04-17 07:11:32.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:32.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:32.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:32.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:32.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:11:32.961][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-04-17 07:11:32.969][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[2024-04-17 07:11:32.989][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:11:32.990][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:11:32.992][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-04-17 07:11:33.435][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-04-17 07:11:33.745][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:11:33.748][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-04-17 07:11:33.764][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-04-17 07:11:33.766][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-04-17 07:11:33.779][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:33.780][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:33.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:33.782][ef$get] fields variable is a list.
biodb.INFO [2024-04-17 07:11:33.787][biodb::testThat]
biodb.INFO [2024-04-17 07:11:33.788][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-04-17 07:11:33.789][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:11:33.790][biodb::testThat]
biodb.TRACE[2024-04-17 07:11:33.815][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:33.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:33.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:33.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:33.820][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:33.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:33.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:33.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:33.823][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:33.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:33.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:33.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:11:33.939][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-04-17 07:11:33.942][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:11:33.957][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-04-17 07:11:33.959][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:11:33.960][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-04-17 07:11:33.978][biodb::testThat]
biodb.INFO [2024-04-17 07:11:33.979][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-04-17 07:11:33.980][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:11:33.981][biodb::testThat]
biodb.TRACE[2024-04-17 07:11:34.002][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:11:34.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:11:34.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.005][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:11:34.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:11:34.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.009][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-17 07:11:34.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-17 07:11:34.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.012][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-17 07:11:34.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-17 07:11:34.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.061][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:11:34.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:11:34.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.065][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:11:34.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:11:34.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.069][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-17 07:11:34.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-17 07:11:34.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.073][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-17 07:11:34.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-17 07:11:34.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-17 07:11:34.083][biodb::testThat]
biodb.INFO [2024-04-17 07:11:34.084][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-04-17 07:11:34.085][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:11:34.086][biodb::testThat]
biodb.INFO [2024-04-17 07:11:34.095][biodb::testThat]
biodb.INFO [2024-04-17 07:11:34.096][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-04-17 07:11:34.097][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:11:34.098][biodb::testThat]
biodb.INFO [2024-04-17 07:11:34.107][biodb::testThat]
biodb.INFO [2024-04-17 07:11:34.108][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-04-17 07:11:34.109][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:11:34.110][biodb::testThat]
biodb.DEBUG[2024-04-17 07:11:34.114][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-04-17 07:11:34.438][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-04-17 07:11:34.539][biodb::testThat]
biodb.INFO [2024-04-17 07:11:34.540][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-04-17 07:11:34.541][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:11:34.542][biodb::testThat]
biodb.TRACE[2024-04-17 07:11:34.548][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:34.550][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:34.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.551][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.552][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:34.553][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:34.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.554][ef$get] fields variable is a list.
biodb.INFO [2024-04-17 07:11:34.557][biodb::testThat]
biodb.INFO [2024-04-17 07:11:34.557][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-04-17 07:11:34.558][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:11:34.559][biodb::testThat]
biodb.TRACE[2024-04-17 07:11:34.570][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:34.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:34.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:34.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:34.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:34.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:34.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:11:34.667][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-04-17 07:11:34.671][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:11:34.685][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-04-17 07:11:34.686][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:11:34.688][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-04-17 07:11:34.749][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-04-17 07:11:34.753][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:11:34.754][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-04-17 07:11:34.755][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:11:34.757][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-04-17 07:11:34.771][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-17 07:11:34.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-17 07:11:34.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:11:34.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:11:34.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:34.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:34.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:34.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:34.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:34.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:34.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:34.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:34.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:34.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:34.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:34.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:34.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:11:34.813][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-04-17 07:11:34.828][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:11:34.829][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:11:34.844][private$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[2024-04-17 07:11:38.592][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[2024-04-17 07:11:43.404][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:11:43.407][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-04-17 07:11:43.418][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-04-17 07:11:44.899][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[2024-04-17 07:11:44.903][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:11:44.904][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:11:44.906][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-04-17 07:11:45.210][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-04-17 07:11:45.503][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:11:45.505][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-04-17 07:11:45.510][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-04-17 07:11:45.533][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-04-17 07:11:45.537][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:11:45.537][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:11:45.539][rule$waitAsNeeded] Wait 0.367072 second(s).
biodb.TRACE[2024-04-17 07:11:46.058][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-04-17 07:11:46.374][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-04-17 07:11:46.651][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:11:46.653][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-04-17 07:11:46.658][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-04-17 07:11:46.674][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-17 07:11:46.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-17 07:11:46.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:46.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-17 07:11:46.685][biodb::testThat]
biodb.INFO [2024-04-17 07:11:46.686][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-04-17 07:11:46.687][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:11:46.688][biodb::testThat]
biodb.TRACE[2024-04-17 07:11:46.691][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-17 07:11:46.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-17 07:11:46.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:46.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:46.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:11:46.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:11:46.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:46.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:46.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:46.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:46.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:46.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:46.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:46.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:46.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:46.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:46.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:46.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:46.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:46.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:46.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:46.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:46.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:46.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:11:46.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:11:46.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:46.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:46.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:46.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:46.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:46.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:46.729][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-04-17 07:11:46.733][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:11:46.734][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:11:46.735][rule$waitAsNeeded] Wait 0.322171 second(s).
biodb.TRACE[2024-04-17 07:11:47.209][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-04-17 07:11:50.811][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-04-17 07:11:55.473][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:11:55.476][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-04-17 07:11:55.488][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-04-17 07:11:56.768][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-04-17 07:11:56.811][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-04-17 07:11:56.813][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-04-17 07:11:56.814][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-04-17 07:11:56.815][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:11:56.816][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:11:56.817][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-17 07:11:56.818][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:11:56.818][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:11:56.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:11:56.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:56.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:56.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:56.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:56.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:56.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:56.844][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-04-17 07:11:56.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:11:56.848][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:11:56.849][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-04-17 07:11:57.134][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-04-17 07:11:57.427][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:11:57.430][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-04-17 07:11:57.434][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-04-17 07:11:57.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:11:57.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:57.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:57.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:57.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:57.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:57.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:57.447][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-04-17 07:11:57.450][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:11:57.451][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:11:57.452][rule$waitAsNeeded] Wait 0.397153 second(s).
biodb.TRACE[2024-04-17 07:11:58.001][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-04-17 07:11:58.315][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-04-17 07:11:58.674][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:11:58.677][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-04-17 07:11:58.681][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-04-17 07:11:58.683][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-04-17 07:11:58.685][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:11:58.686][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-04-17 07:11:58.688][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-17 07:11:58.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:11:58.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:58.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:58.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:58.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:58.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:58.699][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:11:58.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:11:58.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:11:58.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:11:58.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:11:58.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.740][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-17 07:11:58.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-17 07:11:58.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.743][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:11:58.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:11:58.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.747][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:58.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:58.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.750][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:58.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:58.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.753][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:58.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:58.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.756][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:58.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:58.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.760][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-17 07:11:58.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:58.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.763][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-17 07:11:58.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:58.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.766][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:58.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:58.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.769][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:58.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:58.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:58.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:58.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.779][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-17 07:11:58.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.782][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-17 07:11:58.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:58.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:58.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.792][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-17 07:11:58.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.795][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.798][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.805][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:11:58.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:11:58.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:58.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:58.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:58.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:58.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:58.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:11:58.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:11:58.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:11:58.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.844][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-17 07:11:58.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-17 07:11:58.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.847][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:11:58.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:11:58.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.850][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:58.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:58.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.853][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:58.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:11:58.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.857][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:58.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:58.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.875][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:58.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:11:58.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.878][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-17 07:11:58.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:58.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.882][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-17 07:11:58.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:58.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.885][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:58.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:58.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.888][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:11:58.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:11:58.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:58.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.896][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:58.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.899][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-17 07:11:58.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.903][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-17 07:11:58.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:58.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:11:58.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.913][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-17 07:11:58.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:11:58.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.916][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.919][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.926][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:11:58.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:11:58.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:11:58.959][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-04-17 07:11:58.969][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-17 07:11:58.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:11:58.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:58.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:58.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:58.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:58.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:58.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:11:58.982][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.986][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.989][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:11:58.990][private$selectFields]
biodb.TRACE[2024-04-17 07:11:58.991][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:11:58.992][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:11:58.992][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:11:58.993][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.994][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.996][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:58.996][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.997][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:58.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:58.999][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.000][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:11:59.000][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:11:59.001][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.002][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.004][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.004][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-17 07:11:59.020][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.024][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.027][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.039][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-04-17 07:11:59.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:11:59.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:59.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:59.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:59.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:59.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:59.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:11:59.052][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.055][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.058][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:11:59.059][private$selectFields]
biodb.TRACE[2024-04-17 07:11:59.059][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:11:59.060][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:11:59.061][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:11:59.062][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.063][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.064][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.065][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.066][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.067][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.068][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:11:59.069][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:11:59.069][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.070][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.072][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.072][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-17 07:11:59.073][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.076][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.079][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.083][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-04-17 07:11:59.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:11:59.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:59.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:59.090][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:59.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:59.092][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:59.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:11:59.094][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.097][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.100][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:11:59.101][private$selectFields]
biodb.TRACE[2024-04-17 07:11:59.102][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:11:59.102][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:11:59.103][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:11:59.104][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.105][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.106][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.107][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.108][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.110][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.110][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:11:59.111][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:11:59.112][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.113][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.114][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.115][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-17 07:11:59.116][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.119][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.122][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:11:59.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.126][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-04-17 07:11:59.127][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-17 07:11:59.128][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-17 07:11:59.139][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-17 07:11:59.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-17 07:11:59.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-17 07:11:59.147][biodb::testThat]
biodb.INFO [2024-04-17 07:11:59.148][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-04-17 07:11:59.148][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:11:59.149][biodb::testThat]
biodb.TRACE[2024-04-17 07:11:59.152][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-17 07:11:59.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-17 07:11:59.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:11:59.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:11:59.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:59.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:59.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:59.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:59.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:59.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:59.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:11:59.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:59.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:11:59.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:11:59.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:11:59.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:11:59.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:11:59.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:11:59.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:11:59.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:11:59.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:11:59.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:11:59.251][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-04-17 07:11:59.254][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:11:59.255][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:11:59.257][private$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[2024-04-17 07:12:02.781][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[2024-04-17 07:12:06.995][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:12:06.998][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-04-17 07:12:07.009][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-04-17 07:12:08.374][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-17 07:12:08.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:08.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:08.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:08.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:08.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:08.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:08.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:12:08.420][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.423][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.446][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:08.447][private$selectFields]
biodb.TRACE[2024-04-17 07:12:08.448][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:12:08.449][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:12:08.450][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:08.451][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.452][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.454][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.455][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.456][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.457][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.458][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:08.468][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:08.470][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.471][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.473][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.474][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-17 07:12:08.490][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.494][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.497][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.501][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-04-17 07:12:08.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:08.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:08.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:08.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:08.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:08.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:08.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:12:08.514][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.517][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.520][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:08.521][private$selectFields]
biodb.TRACE[2024-04-17 07:12:08.522][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:12:08.523][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:12:08.524][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:08.525][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.525][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.527][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.528][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.528][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.530][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.532][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:08.532][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:08.533][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.534][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.536][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.537][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-17 07:12:08.538][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.541][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.544][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.548][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-04-17 07:12:08.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:08.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:08.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:08.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:08.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:08.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:08.559][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:12:08.560][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.563][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.567][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:08.568][private$selectFields]
biodb.TRACE[2024-04-17 07:12:08.568][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:12:08.569][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:12:08.570][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:08.571][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.571][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.573][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.574][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.574][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.576][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.576][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:08.577][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:08.578][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.579][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.581][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.582][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-17 07:12:08.583][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.586][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.589][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:08.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.593][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-04-17 07:12:08.593][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-17 07:12:08.594][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-17 07:12:08.604][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-17 07:12:08.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-17 07:12:08.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-17 07:12:08.611][biodb::testThat]
biodb.INFO [2024-04-17 07:12:08.612][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-04-17 07:12:08.614][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:12:08.615][biodb::testThat]
biodb.TRACE[2024-04-17 07:12:08.618][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-17 07:12:08.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-17 07:12:08.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-17 07:12:08.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-17 07:12:08.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:12:08.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:12:08.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:12:08.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:12:08.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:12:08.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:12:08.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:08.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:12:08.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:12:08.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:08.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:12:08.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:08.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:08.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:08.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:08.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:08.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:08.670][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[2024-04-17 07:12:08.674][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[2024-04-17 07:12:08.677][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:12:08.678][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-04-17 07:12:08.680][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:12:08.739][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-04-17 07:12:10.296][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-17 07:12:10.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:10.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:10.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:10.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:10.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:10.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:10.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:12:10.310][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.313][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.316][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:10.317][private$selectFields]
biodb.TRACE[2024-04-17 07:12:10.318][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:12:10.319][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:12:10.319][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:10.320][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.321][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.322][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.323][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.324][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.326][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.326][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:10.327][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:10.328][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.329][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.330][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.331][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-17 07:12:10.332][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.335][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.338][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.342][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-04-17 07:12:10.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:10.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:10.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:10.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:10.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:10.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:10.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:12:10.355][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.359][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.362][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:10.363][private$selectFields]
biodb.TRACE[2024-04-17 07:12:10.364][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:12:10.364][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:12:10.365][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:10.366][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.367][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.368][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.369][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.370][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.371][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.372][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:10.373][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:10.374][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.375][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.377][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.378][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-17 07:12:10.379][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.382][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.385][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.390][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-04-17 07:12:10.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:10.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:10.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:10.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:10.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:10.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:10.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:12:10.401][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.405][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.408][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:10.409][private$selectFields]
biodb.TRACE[2024-04-17 07:12:10.409][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-17 07:12:10.410][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:12:10.411][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:10.412][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.413][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.414][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.415][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.416][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.418][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.419][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:10.420][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:12:10.421][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.423][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.425][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.426][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-17 07:12:10.427][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.431][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.434][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:10.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:10.439][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-04-17 07:12:10.720][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-17 07:12:10.721][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-17 07:12:10.740][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-17 07:12:10.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-17 07:12:10.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:10.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-17 07:12:10.747][biodb::testThat]
biodb.INFO [2024-04-17 07:12:10.748][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-04-17 07:12:10.749][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:12:10.750][biodb::testThat]
biodb.DEBUG[2024-04-17 07:12:10.752][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-04-17 07:12:10.753][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-17 07:12:10.755][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-04-17 07:12:10.756][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-17 07:12:10.757][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:12:10.758][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:12:10.759][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-17 07:12:10.760][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:12:10.761][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:12:10.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:10.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:10.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:10.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:10.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:10.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:10.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:10.786][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-04-17 07:12:10.788][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:10.789][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:12:10.791][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-17 07:12:11.087][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:11.088][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:11.089][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[2024-04-17 07:12:11.091][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-17 07:12:11.397][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:11.399][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:11.400][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:11.401][rule$waitAsNeeded] Wait 0.389705 second(s).
biodb.TRACE[2024-04-17 07:12:11.816][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-17 07:12:12.124][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:12.125][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:12.126][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:12.128][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-17 07:12:12.655][private$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[2024-04-17 07:12:12.657][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:12.657][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:12.659][rule$waitAsNeeded] Wait 0.156943 second(s).
biodb.TRACE[2024-04-17 07:12:12.967][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-17 07:12:13.261][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:13.262][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:13.263][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[2024-04-17 07:12:13.264][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-17 07:12:13.548][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:13.550][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:13.551][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:13.552][rule$waitAsNeeded] Wait 0.414316 second(s).
biodb.TRACE[2024-04-17 07:12:14.119][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-17 07:12:14.400][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:14.402][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:14.403][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:14.404][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-17 07:12:14.679][private$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[2024-04-17 07:12:14.680][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:14.681][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:14.682][rule$waitAsNeeded] Wait 0.435946 second(s).
biodb.TRACE[2024-04-17 07:12:15.263][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-17 07:12:15.522][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:15.523][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:15.524][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[2024-04-17 07:12:15.525][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-17 07:12:16.064][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:16.066][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:16.067][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:16.068][rule$waitAsNeeded] Wait 0.194698 second(s).
biodb.TRACE[2024-04-17 07:12:16.414][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-17 07:12:16.702][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:16.703][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:16.704][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:16.705][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-17 07:12:17.239][private$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[2024-04-17 07:12:17.240][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:17.241][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:17.243][rule$waitAsNeeded] Wait 0.170711 second(s).
biodb.TRACE[2024-04-17 07:12:17.565][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-17 07:12:17.861][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:17.863][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:17.864][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[2024-04-17 07:12:17.865][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-17 07:12:18.139][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:18.140][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:18.141][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:18.143][rule$waitAsNeeded] Wait 0.421983 second(s).
biodb.TRACE[2024-04-17 07:12:18.718][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-17 07:12:18.995][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:18.996][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:18.997][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:18.998][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-17 07:12:19.239][private$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[2024-04-17 07:12:19.240][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:19.241][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:19.242][rule$waitAsNeeded] Wait 0.474293 second(s).
biodb.TRACE[2024-04-17 07:12:19.718][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-17 07:12:19.965][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:19.966][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:19.966][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[2024-04-17 07:12:19.967][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-17 07:12:20.197][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:20.198][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:20.198][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:20.199][rule$waitAsNeeded] Wait 0.518616 second(s).
biodb.TRACE[2024-04-17 07:12:20.869][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-17 07:12:21.121][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:21.122][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:21.123][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:21.124][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-17 07:12:21.367][private$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[2024-04-17 07:12:21.370][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-04-17 07:12:21.372][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:12:21.373][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-04-17 07:12:21.375][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-17 07:12:21.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:21.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:21.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:21.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:21.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:21.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:21.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:12:21.389][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:21.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:21.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:21.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:21.413][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:21.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:21.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:21.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:21.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:21.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:21.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:21.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:21.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:21.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:21.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:21.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:21.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:21.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:21.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:21.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:21.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:21.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:21.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:21.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:21.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:21.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:21.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:21.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:21.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:21.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:21.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:21.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:12:21.435][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-04-17 07:12:21.436][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-04-17 07:12:21.444][biodb::testThat]
biodb.INFO [2024-04-17 07:12:21.445][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-04-17 07:12:21.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:12:21.447][biodb::testThat]
biodb.DEBUG[2024-04-17 07:12:21.455][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-04-17 07:12:21.456][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-04-17 07:12:21.458][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-04-17 07:12:21.459][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-04-17 07:12:21.461][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-04-17 07:12:21.462][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-17 07:12:21.463][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:12:21.464][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-17 07:12:21.465][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-17 07:12:21.466][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-17 07:12:21.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:21.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:21.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:21.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:21.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:21.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:21.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:21.481][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-04-17 07:12:21.484][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:21.485][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:21.486][rule$waitAsNeeded] Wait 0.382574 second(s).
biodb.TRACE[2024-04-17 07:12:22.020][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-17 07:12:22.257][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:22.258][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:22.259][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:22.260][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-17 07:12:22.525][private$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[2024-04-17 07:12:22.526][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:22.527][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:22.528][rule$waitAsNeeded] Wait 0.491167 second(s).
biodb.TRACE[2024-04-17 07:12:23.098][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-17 07:12:23.336][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:23.337][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:23.338][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[2024-04-17 07:12:23.339][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-17 07:12:23.583][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:23.584][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:23.585][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:23.586][rule$waitAsNeeded] Wait 0.512032 second(s).
biodb.TRACE[2024-04-17 07:12:24.250][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-17 07:12:24.488][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:24.490][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:24.491][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:24.492][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-17 07:12:24.713][private$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[2024-04-17 07:12:24.714][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:24.715][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:24.716][rule$waitAsNeeded] Wait 0.533091 second(s).
biodb.TRACE[2024-04-17 07:12:25.401][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-17 07:12:25.638][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:25.639][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:25.640][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[2024-04-17 07:12:25.641][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-17 07:12:25.886][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:25.887][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:25.888][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:25.889][rule$waitAsNeeded] Wait 0.510768 second(s).
biodb.TRACE[2024-04-17 07:12:26.552][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-17 07:12:26.799][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:26.800][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:26.801][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:26.803][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-17 07:12:27.048][private$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[2024-04-17 07:12:27.050][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:27.051][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:27.052][rule$waitAsNeeded] Wait 0.499209 second(s).
biodb.TRACE[2024-04-17 07:12:27.703][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-17 07:12:27.981][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:27.982][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:27.983][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[2024-04-17 07:12:27.984][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-17 07:12:28.224][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:28.225][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:28.226][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:28.227][rule$waitAsNeeded] Wait 0.475294 second(s).
biodb.TRACE[2024-04-17 07:12:28.769][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-17 07:12:29.012][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:29.013][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:29.014][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:29.015][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-17 07:12:29.262][private$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[2024-04-17 07:12:29.263][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:29.264][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:29.265][rule$waitAsNeeded] Wait 0.503556 second(s).
biodb.TRACE[2024-04-17 07:12:29.920][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-17 07:12:30.172][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:30.174][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:30.175][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:30.176][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-17 07:12:30.421][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:30.423][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:30.424][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:30.425][rule$waitAsNeeded] Wait 0.495044 second(s).
biodb.TRACE[2024-04-17 07:12:30.993][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-17 07:12:31.273][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:31.274][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:31.275][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:31.276][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-17 07:12:31.525][private$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[2024-04-17 07:12:31.526][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:31.527][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:31.528][rule$waitAsNeeded] Wait 0.464335 second(s).
biodb.TRACE[2024-04-17 07:12:32.144][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-17 07:12:32.412][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:32.413][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:32.414][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[2024-04-17 07:12:32.415][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-17 07:12:32.930][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:32.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:32.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:32.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:32.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:32.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:32.940][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:32.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:32.943][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-04-17 07:12:32.966][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:32.968][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:32.969][rule$waitAsNeeded] Wait 0.174949 second(s).
biodb.TRACE[2024-04-17 07:12:33.295][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-17 07:12:33.521][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:33.522][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:33.524][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:33.525][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-17 07:12:33.749][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:33.751][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:33.752][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:33.753][rule$waitAsNeeded] Wait 0.54185 second(s).
biodb.TRACE[2024-04-17 07:12:34.446][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-17 07:12:34.702][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:34.703][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:34.704][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:34.705][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-17 07:12:34.945][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:34.946][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:34.947][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:34.948][rule$waitAsNeeded] Wait 0.497998 second(s).
biodb.TRACE[2024-04-17 07:12:35.564][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-17 07:12:35.810][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:35.811][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:35.812][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:35.813][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-17 07:12:36.052][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:36.053][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:36.054][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:36.055][rule$waitAsNeeded] Wait 0.508493 second(s).
biodb.TRACE[2024-04-17 07:12:36.716][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-17 07:12:36.966][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:36.968][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:36.969][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:36.970][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-17 07:12:37.234][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:37.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:37.236][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:37.237][rule$waitAsNeeded] Wait 0.478029 second(s).
biodb.TRACE[2024-04-17 07:12:37.864][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-17 07:12:38.100][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:38.101][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:38.102][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:38.103][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-17 07:12:38.346][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:38.348][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:38.348][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:38.349][rule$waitAsNeeded] Wait 0.513805 second(s).
biodb.TRACE[2024-04-17 07:12:39.015][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-17 07:12:39.257][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:39.258][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:39.259][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:39.260][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-17 07:12:39.508][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:39.510][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:39.511][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:39.512][rule$waitAsNeeded] Wait 0.502576 second(s).
biodb.TRACE[2024-04-17 07:12:40.097][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-17 07:12:40.329][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:40.330][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:40.331][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:40.332][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-17 07:12:40.826][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:40.827][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:40.828][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:40.829][rule$waitAsNeeded] Wait 0.267136 second(s).
biodb.TRACE[2024-04-17 07:12:41.216][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-17 07:12:41.458][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:41.459][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:41.460][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:41.461][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-17 07:12:41.769][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:41.771][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:41.772][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:41.773][rule$waitAsNeeded] Wait 0.442488 second(s).
biodb.TRACE[2024-04-17 07:12:42.325][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-17 07:12:42.575][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:42.576][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:42.576][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:42.577][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-17 07:12:42.884][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-17 07:12:42.884][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:42.885][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:42.885][rule$waitAsNeeded] Wait 0.439375 second(s).
biodb.TRACE[2024-04-17 07:12:43.326][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-17 07:12:43.608][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-17 07:12:43.609][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-17 07:12:43.610][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-17 07:12:43.611][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-17 07:12:43.850][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-04-17 07:12:43.853][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-04-17 07:12:43.855][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-17 07:12:43.856][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-04-17 07:12:43.857][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-17 07:12:43.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:43.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:43.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:43.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:43.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:43.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:43.868][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:12:43.870][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:43.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:43.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.873][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:43.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:43.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:43.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:43.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:12:43.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:12:43.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:43.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:43.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:43.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:43.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:43.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:12:43.891][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:43.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:43.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.895][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:43.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:12:43.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:43.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:43.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:43.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:43.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:43.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:43.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:43.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:43.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:43.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:43.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:43.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:43.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:43.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:43.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:43.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:43.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:43.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:43.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:43.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:43.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:43.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:12:43.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:12:43.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:43.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:12:43.957][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-04-17 07:12:43.957][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-04-17 07:12:43.958][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-04-17 07:12:44.168][biodb::testThat]
biodb.INFO [2024-04-17 07:12:44.169][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-04-17 07:12:44.170][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:12:44.171][biodb::testThat]
biodb.INFO [2024-04-17 07:12:44.216][biodb::testThat]
biodb.INFO [2024-04-17 07:12:44.217][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-04-17 07:12:44.218][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:12:44.219][biodb::testThat]
biodb.INFO [2024-04-17 07:12:44.245][biodb::testThat]
biodb.INFO [2024-04-17 07:12:44.246][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-04-17 07:12:44.247][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:12:44.248][biodb::testThat]
biodb.DEBUG[2024-04-17 07:12:44.251][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[2024-04-17 07:12:44.254][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:44.255][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:44.256][rule$waitAsNeeded] Wait 0.0693581 second(s).
biodb.TRACE[2024-04-17 07:12:44.359][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-04-17 07:12:48.100][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-04-17 07:12:52.738][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:12:52.741][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-04-17 07:12:52.751][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-04-17 07:12:54.041][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:12:54.043][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:12:54.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:54.044][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:12:54.045][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:12:54.046][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:12:54.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:12:54.048][ef$get] fields variable is a list.
biodb.INFO [2024-04-17 07:12:54.050][biodb::testThat]
biodb.INFO [2024-04-17 07:12:54.050][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-04-17 07:12:54.051][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:12:54.052][biodb::testThat]
biodb.ERROR[2024-04-17 07:12:54.066][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-04-17 07:12:54.084][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-04-17 07:12:54.099][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-17 07:12:54.101][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-04-17 07:12:54.102][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-04-17 07:12:54.102][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-17 07:12:54.103][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.105][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.106][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-17 07:12:54.118][biodb::testContext]
biodb.INFO [2024-04-17 07:12:54.119][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:12:54.119][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-04-17 07:12:54.120][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:12:54.121][biodb::testContext]
biodb.INFO [2024-04-17 07:12:54.124][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:12:54.125][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-17 07:12:54.131][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:12:54.132][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-17 07:12:54.133][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-17 07:12:54.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.136][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-17 07:12:54.137][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-17 07:12:54.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.140][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-17 07:12:54.141][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-17 07:12:54.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.144][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-17 07:12:54.145][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-17 07:12:54.146][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-17 07:12:54.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.149][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-17 07:12:54.150][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-17 07:12:54.150][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-17 07:12:54.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.172][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-17 07:12:54.173][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-17 07:12:54.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.176][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-17 07:12:54.176][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-17 07:12:54.177][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-17 07:12:54.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.180][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-17 07:12:54.181][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-17 07:12:54.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.184][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-17 07:12:54.185][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-17 07:12:54.185][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-17 07:12:54.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.189][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:12:54.189][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-17 07:12:54.190][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-17 07:12:54.191][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-17 07:12:54.192][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-17 07:12:54.193][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-17 07:12:54.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.195][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-17 07:12:54.196][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-17 07:12:54.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.199][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-17 07:12:54.200][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-17 07:12:54.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.203][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-17 07:12:54.204][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-17 07:12:54.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.206][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-17 07:12:54.207][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-17 07:12:54.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.210][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-17 07:12:54.211][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-17 07:12:54.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.213][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:12:54.214][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-17 07:12:54.230][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-17 07:12:54.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.233][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-17 07:12:54.234][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-17 07:12:54.235][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-17 07:12:54.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.238][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-17 07:12:54.240][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.241][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-17 07:12:54.241][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.242][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:12:54.243][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.244][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.245][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.245][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.246][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:12:54.247][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:12:54.248][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.248][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-17 07:12:54.249][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:12:54.250][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.251][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.252][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:12:54.252][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:12:54.252][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:12:54.252][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:12:54.252][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:12:54.252][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:12:54.253][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:12:54.254][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:12:54.255][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:12:54.255][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:12:54.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:12:54.257][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.258][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.258][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:12:54.259][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:12:54.260][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.260][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.261][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-17 07:12:54.263][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.264][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:12:54.265][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.265][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:12:54.266][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.267][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.268][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.269][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.269][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:12:54.270][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:12:54.271][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.285][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-17 07:12:54.287][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:12:54.287][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.288][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.289][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:12:54.289][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:12:54.289][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:12:54.289][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:12:54.289][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:12:54.290][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:12:54.291][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:12:54.291][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:12:54.292][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:12:54.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:12:54.294][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:12:54.294][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.295][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.296][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:12:54.297][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:12:54.297][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.298][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.299][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-17 07:12:54.301][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.302][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-17 07:12:54.302][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.303][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:12:54.304][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.305][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.306][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.307][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.308][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:12:54.309][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:12:54.309][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.310][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-17 07:12:54.311][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:12:54.312][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.313][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.313][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.314][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:12:54.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:12:54.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:12:54.316][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:12:54.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:12:54.318][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:12:54.319][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.319][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.320][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:12:54.321][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:12:54.321][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.322][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.323][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-17 07:12:54.325][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.326][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:12:54.326][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.327][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:12:54.328][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.329][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.330][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.330][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.331][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:12:54.332][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:12:54.333][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.334][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-17 07:12:54.334][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:12:54.335][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.336][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.337][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.337][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:12:54.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:12:54.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:12:54.340][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:12:54.340][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:12:54.342][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:12:54.343][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.344][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.345][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:12:54.346][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:12:54.346][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.347][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.348][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:12:54.349][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.371][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[2024-04-17 07:12:54.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.401][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[2024-04-17 07:12:54.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.405][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[2024-04-17 07:12:54.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.417][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.DEBUG[2024-04-17 07:12:54.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.420][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[2024-04-17 07:12:54.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.427][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[2024-04-17 07:12:54.428][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-17 07:12:54.429][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-17 07:12:54.430][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-17 07:12:54.431][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-17 07:12:54.433][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-17 07:12:54.434][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-17 07:12:54.435][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-17 07:12:54.436][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-17 07:12:54.437][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-17 07:12:54.438][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-17 07:12:54.439][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-17 07:12:54.440][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-17 07:12:54.441][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-17 07:12:54.442][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-17 07:12:54.444][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-17 07:12:54.445][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-17 07:12:54.446][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-17 07:12:54.447][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-17 07:12:54.448][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-17 07:12:54.449][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-17 07:12:54.450][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-17 07:12:54.451][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-17 07:12:54.453][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-17 07:12:54.454][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-17 07:12:54.455][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-17 07:12:54.456][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-17 07:12:54.457][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-17 07:12:54.458][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-17 07:12:54.459][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-17 07:12:54.461][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-17 07:12:54.462][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-17 07:12:54.463][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-17 07:12:54.464][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-17 07:12:54.465][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-17 07:12:54.466][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-17 07:12:54.467][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-17 07:12:54.468][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-17 07:12:54.469][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-17 07:12:54.471][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-17 07:12:54.472][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-17 07:12:54.473][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-17 07:12:54.474][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-17 07:12:54.475][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-17 07:12:54.476][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-17 07:12:54.477][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-17 07:12:54.478][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-17 07:12:54.493][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-17 07:12:54.495][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-17 07:12:54.496][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-17 07:12:54.497][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-17 07:12:54.498][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-17 07:12:54.499][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-17 07:12:54.500][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-17 07:12:54.501][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-17 07:12:54.503][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-17 07:12:54.504][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-17 07:12:54.505][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-17 07:12:54.506][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-17 07:12:54.507][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-17 07:12:54.508][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-17 07:12:54.509][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-17 07:12:54.510][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-17 07:12:54.512][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-17 07:12:54.513][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-17 07:12:54.514][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-17 07:12:54.515][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-17 07:12:54.516][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-17 07:12:54.517][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-17 07:12:54.518][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-17 07:12:54.520][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-17 07:12:54.521][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-17 07:12:54.522][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-17 07:12:54.523][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-17 07:12:54.524][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-17 07:12:54.525][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-17 07:12:54.526][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-17 07:12:54.527][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-17 07:12:54.528][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-17 07:12:54.529][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-17 07:12:54.530][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-17 07:12:54.532][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-17 07:12:54.533][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-17 07:12:54.534][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-17 07:12:54.539][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-17 07:12:54.541][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:12:54.542][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:12:54.543][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.544][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.545][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[2024-04-17 07:12:54.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.555][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[2024-04-17 07:12:54.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:12:54.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:12:54.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:12:54.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:12:54.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:12:54.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:12:54.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:12:54.640][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[2024-04-17 07:12:54.642][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-04-17 07:12:54.644][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-04-17 07:12:54.645][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.646][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.647][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.648][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:12:54.649][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.649][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.650][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.651][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.652][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:12:54.653][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:12:54.653][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.654][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-04-17 07:12:54.655][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:12:54.656][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-04-17 07:12:54.656][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-04-17 07:12:54.656][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-04-17 07:12:54.656][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-04-17 07:12:54.656][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-04-17 07:12:54.656][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-04-17 07:12:54.656][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-04-17 07:12:54.656][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-04-17 07:12:54.656][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-04-17 07:12:54.657][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-17 07:12:54.657][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:12:54.657][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:12:54.658][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:12:54.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:12:54.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:12:54.660][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:12:54.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:12:54.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:12:54.663][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:12:54.663][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-17 07:12:54.663][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-04-17 07:12:54.664][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:12:54.665][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:12:54.666][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-17 07:12:54.666][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:12:54.667][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-04-17 07:12:54.669][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-17 07:12:54.672][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-04-17 07:12:54.673][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-04-17 07:12:54.674][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-04-17 07:12:54.675][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-04-17 07:12:54.676][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-17 07:12:54.677][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-17 07:12:54.678][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-04-17 07:12:54.692][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-04-17 07:12:54.694][biodb::testThat]
biodb.INFO [2024-04-17 07:12:54.695][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-04-17 07:12:54.696][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:12:54.697][biodb::testThat]
biodb.DEBUG[2024-04-17 07:12:54.700][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[2024-04-17 07:12:54.705][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:54.706][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:12:54.707][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-04-17 07:12:55.015][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-04-17 07:12:55.307][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:12:55.310][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-04-17 07:12:55.314][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-04-17 07:12:55.325][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-04-17 07:12:55.328][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:55.329][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:55.330][rule$waitAsNeeded] Wait 0.376496 second(s).
biodb.TRACE[2024-04-17 07:12:55.859][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-04-17 07:12:56.168][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-04-17 07:12:56.445][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:12:56.447][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-04-17 07:12:56.452][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-04-17 07:12:56.463][biodb::testThat]
biodb.INFO [2024-04-17 07:12:56.464][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-04-17 07:12:56.465][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:12:56.466][biodb::testThat]
biodb.INFO [2024-04-17 07:12:56.493][biodb::testThat]
biodb.INFO [2024-04-17 07:12:56.494][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-04-17 07:12:56.495][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:12:56.496][biodb::testThat]
biodb.DEBUG[2024-04-17 07:12:56.498][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-04-17 07:12:56.502][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:56.502][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:56.503][rule$waitAsNeeded] Wait 0.354488 second(s).
biodb.TRACE[2024-04-17 07:12:56.942][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-04-17 07:12:57.090][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-04-17 07:12:57.250][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:12:57.253][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-04-17 07:12:57.257][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-04-17 07:12:57.283][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-04-17 07:12:57.287][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:12:57.288][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-04-17 07:12:57.289][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:12:57.290][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-04-17 07:12:57.296][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-04-17 07:12:57.300][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:57.300][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:57.301][rule$waitAsNeeded] Wait 0.640066 second(s).
biodb.TRACE[2024-04-17 07:12:58.029][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-04-17 07:12:58.173][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-04-17 07:12:58.322][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:12:58.324][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-04-17 07:12:58.328][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-04-17 07:12:58.337][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-04-17 07:12:58.340][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:12:58.341][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-17 07:12:58.343][rule$waitAsNeeded] Wait 0.684912 second(s).
biodb.TRACE[2024-04-17 07:12:59.114][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-04-17 07:13:00.079][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-04-17 07:13:01.122][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:13:01.124][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-04-17 07:13:01.129][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-04-17 07:13:01.312][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-04-17 07:13:01.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-17 07:13:01.316][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-17 07:13:01.317][private$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[2024-04-17 07:13:02.210][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[2024-04-17 07:13:03.284][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-17 07:13:03.287][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-04-17 07:13:03.292][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-04-17 07:13:03.524][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-17 07:13:03.525][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-04-17 07:13:03.526][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-04-17 07:13:03.527][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-17 07:13:03.528][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:03.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:03.529][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.531][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.531][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.INFO [2024-04-17 07:13:03.535][biodb::testContext]
biodb.INFO [2024-04-17 07:13:03.536][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:13:03.537][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-04-17 07:13:03.538][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-17 07:13:03.539][biodb::testContext]
biodb.INFO [2024-04-17 07:13:03.541][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:13:03.543][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-17 07:13:03.549][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:13:03.550][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-17 07:13:03.551][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-17 07:13:03.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.554][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-17 07:13:03.555][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-17 07:13:03.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.558][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-17 07:13:03.559][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-17 07:13:03.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.562][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-17 07:13:03.563][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-17 07:13:03.564][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-17 07:13:03.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.566][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[2024-04-17 07:13:03.566][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-17 07:13:03.567][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-17 07:13:03.568][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-17 07:13:03.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.571][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-17 07:13:03.572][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-17 07:13:03.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.575][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-17 07:13:03.576][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-17 07:13:03.577][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-17 07:13:03.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.580][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-17 07:13:03.581][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-17 07:13:03.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.584][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-17 07:13:03.585][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-17 07:13:03.586][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-17 07:13:03.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.589][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:13:03.590][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-17 07:13:03.591][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-17 07:13:03.592][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-17 07:13:03.593][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-17 07:13:03.594][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-17 07:13:03.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.597][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-17 07:13:03.598][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-17 07:13:03.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.600][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-17 07:13:03.601][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-17 07:13:03.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.604][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-17 07:13:03.605][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-17 07:13:03.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.608][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-17 07:13:03.609][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-17 07:13:03.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.612][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-17 07:13:03.612][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-17 07:13:03.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.615][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-17 07:13:03.616][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-17 07:13:03.648][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-17 07:13:03.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.651][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-17 07:13:03.652][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-17 07:13:03.653][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-17 07:13:03.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.656][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-17 07:13:03.658][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:03.658][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-17 07:13:03.660][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.661][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:13:03.662][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.663][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:13:03.663][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:03.664][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:13:03.665][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:13:03.666][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:13:03.667][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.668][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-17 07:13:03.669][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:13:03.669][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.670][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.672][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:13:03.672][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:13:03.672][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:13:03.672][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:13:03.672][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:13:03.673][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:13:03.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:13:03.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:13:03.675][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:13:03.676][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:13:03.677][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:13:03.678][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:13:03.679][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.679][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:13:03.680][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:13:03.681][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:03.682][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.683][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-17 07:13:03.685][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:03.686][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:13:03.687][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.688][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:13:03.689][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.690][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:13:03.691][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:03.692][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:13:03.692][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:13:03.693][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:13:03.694][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.695][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-17 07:13:03.697][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:13:03.698][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.698][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.699][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:13:03.699][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:13:03.699][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-17 07:13:03.699][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-17 07:13:03.699][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-17 07:13:03.700][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:13:03.701][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:13:03.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:13:03.703][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:13:03.703][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:13:03.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:13:03.705][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:13:03.706][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.706][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:13:03.707][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:13:03.708][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:03.709][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.710][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-17 07:13:03.711][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.712][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-17 07:13:03.713][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.714][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:13:03.715][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.716][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:13:03.717][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:03.718][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:13:03.718][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:13:03.719][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:13:03.720][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:03.721][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-17 07:13:03.722][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:13:03.722][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.723][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.724][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.725][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:13:03.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:13:03.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:13:03.727][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:13:03.728][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:13:03.728][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:13:03.729][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:13:03.730][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.731][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:13:03.731][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:13:03.732][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:03.733][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.734][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-17 07:13:03.736][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.736][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-17 07:13:03.737][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.738][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:13:03.739][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.740][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:13:03.741][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:03.757][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:13:03.758][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-17 07:13:03.759][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:13:03.759][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:03.760][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-17 07:13:03.761][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:13:03.762][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.763][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:03.763][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.764][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:13:03.765][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:13:03.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:13:03.766][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:13:03.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:13:03.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:13:03.769][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:13:03.769][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.770][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:13:03.771][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:13:03.772][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:03.772][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:03.774][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:13:03.774][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.791][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.DEBUG[2024-04-17 07:13:03.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.821][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[2024-04-17 07:13:03.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.841][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-17 07:13:03.842][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-17 07:13:03.843][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-17 07:13:03.844][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-17 07:13:03.860][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-17 07:13:03.862][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-17 07:13:03.863][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-17 07:13:03.864][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-17 07:13:03.865][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-17 07:13:03.866][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-17 07:13:03.868][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-17 07:13:03.869][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-17 07:13:03.870][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-17 07:13:03.871][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-17 07:13:03.872][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-17 07:13:03.873][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-17 07:13:03.874][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-17 07:13:03.876][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-17 07:13:03.877][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-17 07:13:03.879][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-17 07:13:03.880][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-17 07:13:03.881][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-17 07:13:03.882][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-17 07:13:03.884][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-17 07:13:03.885][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-17 07:13:03.886][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-17 07:13:03.887][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-17 07:13:03.888][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-17 07:13:03.889][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-17 07:13:03.891][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-17 07:13:03.892][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-17 07:13:03.894][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-17 07:13:03.895][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-17 07:13:03.896][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-17 07:13:03.897][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-17 07:13:03.899][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-17 07:13:03.900][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-17 07:13:03.901][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-17 07:13:03.902][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-17 07:13:03.903][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-17 07:13:03.904][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-17 07:13:03.905][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-17 07:13:03.907][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-17 07:13:03.908][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-17 07:13:03.909][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-17 07:13:03.911][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-17 07:13:03.912][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-17 07:13:03.913][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-17 07:13:03.914][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-17 07:13:03.915][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-17 07:13:03.917][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-17 07:13:03.918][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-17 07:13:03.919][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-17 07:13:03.920][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-17 07:13:03.921][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-17 07:13:03.922][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-17 07:13:03.923][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-17 07:13:03.924][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-17 07:13:03.926][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-17 07:13:03.927][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-17 07:13:03.929][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-17 07:13:03.930][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-17 07:13:03.932][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-17 07:13:03.933][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-17 07:13:03.934][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-17 07:13:03.936][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-17 07:13:03.937][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-17 07:13:03.938][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-17 07:13:03.939][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-17 07:13:03.940][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-17 07:13:03.941][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-17 07:13:03.943][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-17 07:13:03.944][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-17 07:13:03.945][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-17 07:13:03.946][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-17 07:13:03.948][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-17 07:13:03.949][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-17 07:13:03.965][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-17 07:13:03.967][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-17 07:13:03.968][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-17 07:13:03.969][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-17 07:13:03.970][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-17 07:13:03.971][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-17 07:13:03.973][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-17 07:13:03.974][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-17 07:13:03.975][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-17 07:13:03.976][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.978][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:03.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:03.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:03.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:03.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:03.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:03.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:03.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:03.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:03.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:03.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:03.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:03.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:03.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.046][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[2024-04-17 07:13:04.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-17 07:13:04.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:04.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:04.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:04.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:04.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:04.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-17 07:13:04.082][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-04-17 07:13:04.084][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-04-17 07:13:04.086][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:04.087][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-17 07:13:04.087][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:04.088][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-17 07:13:04.089][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:04.090][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-17 07:13:04.091][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:04.091][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-17 07:13:04.092][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-17 07:13:04.093][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-17 07:13:04.094][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:04.095][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-04-17 07:13:04.095][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-17 07:13:04.096][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-04-17 07:13:04.096][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-04-17 07:13:04.096][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-04-17 07:13:04.096][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-04-17 07:13:04.096][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-04-17 07:13:04.096][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-04-17 07:13:04.096][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-04-17 07:13:04.096][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-04-17 07:13:04.096][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-04-17 07:13:04.097][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-17 07:13:04.098][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-17 07:13:04.098][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-17 07:13:04.099][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-17 07:13:04.099][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:13:04.100][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:13:04.101][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-17 07:13:04.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-17 07:13:04.102][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-17 07:13:04.103][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-17 07:13:04.104][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-17 07:13:04.104][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-04-17 07:13:04.105][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-17 07:13:04.105][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-17 07:13:04.106][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-17 07:13:04.107][self$setPropertyValue]
biodb.DEBUG[2024-04-17 07:13:04.108][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-04-17 07:13:04.109][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-17 07:13:04.112][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-04-17 07:13:04.113][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-04-17 07:13:04.114][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-04-17 07:13:04.115][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-04-17 07:13:04.116][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-17 07:13:04.117][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-17 07:13:04.118][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-04-17 07:13:04.119][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-04-17 07:13:04.121][biodb::testThat]
biodb.INFO [2024-04-17 07:13:04.122][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-04-17 07:13:04.122][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-17 07:13:04.123][biodb::testThat]
biodb.DEBUG[2024-04-17 07:13:04.127][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[2024-04-17 07:13:04.131][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-17 07:13:04.132][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-04-17 07:13:04.133][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-17 07:13:04.202][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-04-17 07:13:05.859][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-04-17 07:13:05.860][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-04-17 07:13:05.862][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-04-17 07:13:05.863][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-04-17 07:13:05.865][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[2024-04-17 07:13:05.866][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-17 07:13:05.867][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-04-17 07:13:05.868][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-17 07:13:05.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:13:05.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:05.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:05.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:05.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:05.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:05.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:13:05.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:05.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:05.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:05.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:05.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:05.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:05.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:05.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:05.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.898][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-17 07:13:05.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-17 07:13:05.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.902][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:13:05.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:13:05.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.905][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:05.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:05.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.908][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:05.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:05.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.911][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:05.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:05.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.915][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:05.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:05.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.918][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-17 07:13:05.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:05.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.921][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-17 07:13:05.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:05.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.924][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:05.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:05.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.927][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:05.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:05.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:05.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:05.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.934][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:05.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:05.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.937][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-17 07:13:05.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:05.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.940][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-17 07:13:05.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:05.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:05.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:05.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:05.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:05.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.949][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-17 07:13:05.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:05.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:05.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:05.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:05.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:05.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:05.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:05.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:05.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:05.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:05.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:05.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.968][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:05.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:05.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.971][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:05.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:05.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:05.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:05.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.977][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:05.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:05.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:05.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:05.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:05.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:05.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:05.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:05.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:05.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:05.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:13:05.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:13:05.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:05.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:06.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:06.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:06.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:06.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:13:06.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.024][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-17 07:13:06.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-17 07:13:06.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.028][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:13:06.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-17 07:13:06.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.032][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.035][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.039][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.043][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.046][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-17 07:13:06.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.050][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-17 07:13:06.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.059][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.071][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-17 07:13:06.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.075][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-17 07:13:06.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.082][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.086][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-17 07:13:06.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.090][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.093][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.102][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-17 07:13:06.140][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-04-17 07:13:06.143][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-17 07:13:06.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:13:06.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:06.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:06.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:06.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:06.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:06.158][FUN] Functions in observer BiodbConfig: [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[2024-04-17 07:13:06.160][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:13:06.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:13:06.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.164][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:13:06.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:13:06.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-17 07:13:06.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-17 07:13:06.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.172][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-17 07:13:06.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-17 07:13:06.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.176][private$selectFields] Fields none
biodb.TRACE[2024-04-17 07:13:06.177][private$selectFields]
biodb.TRACE[2024-04-17 07:13:06.177][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-04-17 07:13:06.178][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:13:06.179][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:13:06.180][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.181][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.183][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.184][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.185][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.186][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.187][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.188][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.190][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.191][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.192][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.194][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.194][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.195][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.197][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.198][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.199][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.201][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.201][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.202][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.204][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.205][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.206][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.208][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.209][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.210][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.211][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.212][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.213][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.215][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.216][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.217][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.218][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.219][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.220][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.222][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.223][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.224][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.226][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.227][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.252][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.254][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.255][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.256][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.257][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.258][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.259][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.260][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.261][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:13:06.262][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:13:06.263][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.264][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.265][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.266][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.267][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.268][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.269][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.270][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.271][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.272][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.273][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.275][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.275][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.276][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.278][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.278][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.279][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.281][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.281][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.282][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.284][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.284][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.285][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.287][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.288][private$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[2024-04-17 07:13:06.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.308][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.312][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.315][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.319][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.322][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.338][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.341][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.344][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.348][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.357][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.361][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.364][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.375][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-04-17 07:13:06.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-17 07:13:06.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:06.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:06.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:06.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:06.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:06.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-17 07:13:06.388][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:13:06.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:13:06.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.392][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-17 07:13:06.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-17 07:13:06.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.395][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-17 07:13:06.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-17 07:13:06.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.399][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-17 07:13:06.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-17 07:13:06.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.402][private$selectFields] Fields none
biodb.TRACE[2024-04-17 07:13:06.403][private$selectFields]
biodb.TRACE[2024-04-17 07:13:06.404][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-04-17 07:13:06.404][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-17 07:13:06.405][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:13:06.406][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.407][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.408][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.409][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.410][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.411][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.412][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.413][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.415][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.415][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.416][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.418][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.418][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.419][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.421][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.422][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.422][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.424][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.425][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.426][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.427][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.428][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.429][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.430][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.431][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.432][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.433][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.434][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.435][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.436][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.437][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.438][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.440][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.440][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.441][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.443][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.444][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.444][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.446][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.447][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.448][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.450][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.450][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.451][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.453][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.454][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.454][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.456][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.457][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:13:06.458][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-04-17 07:13:06.458][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.459][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.461][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.461][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.462][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.464][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.464][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.465][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.467][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.468][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.468][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.470][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.471][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.472][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.473][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.474][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.475][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.476][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.477][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.478][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.479][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.480][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.481][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.482][ef$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.483][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-04-17 07:13:06.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-17 07:13:06.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-17 07:13:06.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-17 07:13:06.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.504][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.507][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.510][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-17 07:13:06.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.517][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.521][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-17 07:13:06.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-17 07:13:06.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.535][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.538][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.541][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-17 07:13:06.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-17 07:13:06.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-17 07:13:06.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-17 07:13:06.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.554][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.557][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.560][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-17 07:13:06.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-17 07:13:06.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-17 07:13:06.567][private$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[2024-04-17 07:13:06.568][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-04-17 07:13:06.569][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-04-17 07:13:06.575][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-17 07:13:06.577][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-04-17 07:13:06.578][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-04-17 07:13:06.579][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-17 07:13:06.580][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-17 07:13:06.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-17 07:13:06.581][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-17 07:13:06.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-17 07:13:06.582][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-17 07:13:06.583][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".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_100_generic.R:16:1'): One wrong entry does not block the retrieval of good ones ──
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
One of the entries is NULL.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.5370.5583.751
LipidmapsStructureEntry0.3540.0160.373