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This page was generated on 2024-03-29 11:35:48 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 200/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 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)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for biodbLipidmaps on nebbiolo2


To the developers/maintainers of the biodbLipidmaps package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: biodbLipidmaps
Version: 1.8.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings biodbLipidmaps_1.8.0.tar.gz
StartedAt: 2024-03-27 20:35:17 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 20:40:24 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 306.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings biodbLipidmaps_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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 ...
  ‘biodbLipidmaps.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-03-27 20:35:58.547][biodb::testContext]
biodb.INFO [2024-03-27 20:35:58.549][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:35:58.550][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-03-27 20:35:58.551][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:35:58.552][biodb::testContext]
biodb.INFO [2024-03-27 20:35:58.560][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-27 20:35:58.562][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 20:35:58.570][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:35:58.571][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 20:35:58.572][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 20:35:58.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.576][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 20:35:58.596][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 20:35:58.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.600][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 20:35:58.601][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 20:35:58.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.604][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 20:35:58.606][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 20:35:58.607][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 20:35:58.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.610][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 20:35:58.611][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 20:35:58.613][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 20:35:58.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.616][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 20:35:58.617][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 20:35:58.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.621][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 20:35:58.622][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 20:35:58.623][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 20:35:58.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.627][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 20:35:58.628][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 20:35:58.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.631][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[2024-03-27 20:35:58.632][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 20:35:58.633][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 20:35:58.634][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 20:35:58.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.638][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:35:58.639][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 20:35:58.640][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 20:35:58.641][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 20:35:58.642][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 20:35:58.643][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 20:35:58.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.647][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 20:35:58.648][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 20:35:58.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.651][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 20:35:58.653][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 20:35:58.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.655][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[2024-03-27 20:35:58.656][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 20:35:58.657][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 20:35:58.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.661][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 20:35:58.662][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 20:35:58.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.666][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 20:35:58.667][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 20:35:58.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.671][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:35:58.672][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 20:35:58.676][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 20:35:58.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.678][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[2024-03-27 20:35:58.679][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 20:35:58.681][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 20:35:58.682][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 20:35:58.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.688][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 20:35:58.725][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:58.749][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-27 20:35:58.750][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.751][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:35:58.752][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.753][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:35:58.754][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:58.755][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:35:58.756][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:35:58.756][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:35:58.757][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.758][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 20:35:58.759][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:35:58.760][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.761][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.762][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:35:58.762][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:35:58.762][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:35:58.762][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:35:58.762][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:35:58.763][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:35:58.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:35:58.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:35:58.765][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:35:58.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:35:58.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:35:58.768][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:35:58.769][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.770][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:35:58.771][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:35:58.772][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:58.772][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.774][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 20:35:58.775][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:58.776][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:35:58.777][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.783][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:35:58.784][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.785][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:35:58.787][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:58.788][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:35:58.789][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:35:58.790][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:35:58.791][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.792][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 20:35:58.793][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:35:58.794][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.795][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.796][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:35:58.796][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:35:58.796][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:35:58.796][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:35:58.796][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:35:58.797][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:35:58.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:35:58.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:35:58.800][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:35:58.801][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:35:58.802][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:35:58.803][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:35:58.804][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.805][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:35:58.806][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:35:58.807][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:58.808][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.809][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 20:35:58.811][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.813][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-27 20:35:58.814][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.815][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:35:58.816][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.817][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:35:58.818][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:58.819][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:35:58.820][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:35:58.821][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:35:58.822][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:58.823][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 20:35:58.824][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:35:58.825][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.826][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.827][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.828][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:35:58.829][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:35:58.830][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:35:58.831][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:35:58.832][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:35:58.833][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:35:58.834][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:35:58.835][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.836][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:35:58.837][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:35:58.838][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:58.839][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.840][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 20:35:58.842][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.843][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:35:58.844][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.845][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:35:58.846][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.847][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:35:58.848][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:58.849][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:35:58.850][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:35:58.851][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:35:58.852][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:58.853][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 20:35:58.854][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:35:58.855][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.856][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:58.857][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.858][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:35:58.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:35:58.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:35:58.861][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:35:58.862][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:35:58.863][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:35:58.864][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:35:58.865][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.866][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:35:58.866][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:35:58.867][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:58.868][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:58.873][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:35:58.874][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.889][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.DEBUG[2024-03-27 20:35:58.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.902][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[2024-03-27 20:35:58.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.911][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[2024-03-27 20:35:58.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.916][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[2024-03-27 20:35:58.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.925][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[2024-03-27 20:35:58.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:58.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:58.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:58.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:58.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:58.953][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 20:35:58.959][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 20:35:58.960][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 20:35:58.962][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 20:35:58.963][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:35:58.964][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 20:35:58.966][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 20:35:58.967][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 20:35:58.968][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 20:35:58.970][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 20:35:58.971][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:35:58.973][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 20:35:58.974][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 20:35:58.975][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 20:35:58.977][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 20:35:58.978][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:35:58.980][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 20:35:58.981][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 20:35:58.982][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:35:58.984][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 20:35:58.985][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 20:35:58.987][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 20:35:58.988][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 20:35:58.990][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 20:35:58.991][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 20:35:58.992][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 20:35:58.994][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 20:35:58.995][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 20:35:58.996][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 20:35:58.998][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 20:35:58.999][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 20:35:59.001][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 20:35:59.002][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 20:35:59.016][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 20:35:59.017][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 20:35:59.019][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 20:35:59.020][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 20:35:59.022][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 20:35:59.023][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 20:35:59.024][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 20:35:59.026][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 20:35:59.027][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 20:35:59.029][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 20:35:59.030][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 20:35:59.031][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 20:35:59.033][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 20:35:59.034][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 20:35:59.036][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 20:35:59.037][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 20:35:59.038][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 20:35:59.040][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 20:35:59.041][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 20:35:59.043][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 20:35:59.044][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 20:35:59.045][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 20:35:59.047][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 20:35:59.048][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 20:35:59.050][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 20:35:59.051][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 20:35:59.052][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 20:35:59.054][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 20:35:59.055][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 20:35:59.056][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 20:35:59.057][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 20:35:59.059][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 20:35:59.060][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 20:35:59.061][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:35:59.063][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:35:59.064][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 20:35:59.065][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 20:35:59.067][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 20:35:59.068][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 20:35:59.069][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 20:35:59.070][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 20:35:59.072][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 20:35:59.073][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 20:35:59.074][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 20:35:59.076][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 20:35:59.077][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 20:35:59.078][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 20:35:59.079][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 20:35:59.081][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 20:35:59.082][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 20:35:59.088][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 20:35:59.089][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-27 20:35:59.093][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:35:59.094][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.095][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.158][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.DEBUG[2024-03-27 20:35:59.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.175][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[2024-03-27 20:35:59.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:35:59.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:35:59.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.198][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[2024-03-27 20:35:59.200][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-27 20:35:59.209][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:35:59.211][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:59.211][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 20:35:59.212][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:59.213][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:35:59.214][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:59.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:35:59.216][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:59.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:35:59.218][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:35:59.219][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:35:59.220][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:59.221][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-27 20:35:59.222][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:35:59.223][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-27 20:35:59.223][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-27 20:35:59.223][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-27 20:35:59.223][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-27 20:35:59.223][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-27 20:35:59.223][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-27 20:35:59.223][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-27 20:35:59.223][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-27 20:35:59.223][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-27 20:35:59.224][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 20:35:59.224][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:35:59.224][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:35:59.225][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:35:59.226][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:35:59.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:35:59.228][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:35:59.229][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:35:59.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:35:59.231][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:35:59.232][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 20:35:59.232][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-27 20:35:59.232][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:35:59.233][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:35:59.234][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 20:35:59.235][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:35:59.241][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-27 20:35:59.242][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:35:59.273][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:35:59.274][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-27 20:35:59.278][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:35:59.283][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-27 20:35:59.287][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 20:35:59.288][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 20:35:59.289][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-27 20:35:59.290][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-27 20:35:59.300][biodb::testThat]
biodb.INFO [2024-03-27 20:35:59.301][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-03-27 20:35:59.301][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:35:59.302][biodb::testThat]
biodb.TRACE[2024-03-27 20:35:59.306][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-03-27 20:35:59.307][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:35:59.311][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 20:35:59.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:35:59.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:35:59.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:35:59.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:35:59.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.372][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:35:59.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:35:59.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.376][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:35:59.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:35:59.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.380][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.408][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.412][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.416][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.420][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:35:59.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.424][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:35:59.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.428][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:35:59.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:35:59.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.431][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:35:59.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:35:59.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.443][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:35:59.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.447][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 20:35:59.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.458][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:35:59.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.478][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.525][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.536][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.540][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.547][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:35:59.573][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-27 20:35:59.575][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:35:59.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:35:59.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.579][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:35:59.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:35:59.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.583][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:35:59.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:35:59.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.586][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:35:59.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:35:59.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.619][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.651][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.654][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.658][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:35:59.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.679][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.680][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.682][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.705][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.706][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.708][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.713][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.724][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.728][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.731][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.735][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.736][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.738][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.739][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.749][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:35:59.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:35:59.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.753][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:35:59.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:35:59.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.757][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:35:59.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:35:59.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.760][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:35:59.761][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:35:59.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.763][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.764][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:35:59.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:35:59.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.786][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.787][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.789][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.800][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.804][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.808][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.811][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.812][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.814][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.815][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.826][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.827][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.829][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.833][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.834][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.835][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.839][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:35:59.840][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:35:59.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.842][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.846][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.847][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:35:59.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.849][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.853][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:35:59.854][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:35:59.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.855][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.859][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.860][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.862][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 20:35:59.869][biodb::testThat]
biodb.INFO [2024-03-27 20:35:59.870][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-27 20:35:59.871][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:35:59.872][biodb::testThat]
biodb.DEBUG[2024-03-27 20:35:59.884][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-03-27 20:35:59.891][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:35:59.896][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-03-27 20:35:59.897][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:35:59.898][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-03-27 20:35:59.899][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:35:59.947][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:35:59.949][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 20:35:59.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:35:59.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:35:59.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:35:59.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:35:59.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:35:59.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:35:59.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:35:59.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:35:59.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:35:59.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:35:59.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:35:59.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:35:59.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:35:59.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.978][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:35:59.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:35:59.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.982][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:35:59.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:35:59.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.985][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.989][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:35:59.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.993][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:35:59.996][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:35:59.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:35:59.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.000][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:36:00.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:00.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.004][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:36:00.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:00.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.008][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:36:00.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:36:00.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.011][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:36:00.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:36:00.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.023][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:36:00.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.027][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 20:36:00.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.030][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.038][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:36:00.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.053][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.060][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:00.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:00.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.064][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:00.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:00.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:00.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:00.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.071][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:00.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:00.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:00.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:00.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:00.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:00.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:00.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:00.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:00.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:00.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:00.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:00.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:00.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:00.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:36:00.097][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-27 20:36:00.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-27 20:36:00.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-27 20:36:00.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-27 20:36:00.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-27 20:36:00.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-27 20:36:00.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-27 20:36:00.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:36:00.115][biodb::testThat]
biodb.INFO [2024-03-27 20:36:00.116][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-27 20:36:00.117][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:36:00.118][biodb::testThat]
biodb.TRACE[2024-03-27 20:36:00.121][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.122][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.124][ef$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:36:00.125][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-03-27 20:36:00.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.156][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:00.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:00.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:00.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:00.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:36:00.166][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 20:36:00.171][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[2024-03-27 20:36:00.191][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:36:00.192][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:36:00.193][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-03-27 20:36:00.970][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-03-27 20:36:01.659][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:36:01.664][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-03-27 20:36:01.698][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-03-27 20:36:01.702][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-03-27 20:36:01.734][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:01.735][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:01.736][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:01.737][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 20:36:01.742][biodb::testThat]
biodb.INFO [2024-03-27 20:36:01.743][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-03-27 20:36:01.744][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:36:01.745][biodb::testThat]
biodb.TRACE[2024-03-27 20:36:01.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:01.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:01.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:01.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:01.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:01.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:01.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:01.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:01.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:01.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:01.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:01.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:36:01.880][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 20:36:01.890][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:36:01.906][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-27 20:36:01.907][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:36:01.908][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-03-27 20:36:01.924][biodb::testThat]
biodb.INFO [2024-03-27 20:36:01.925][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-03-27 20:36:01.926][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:36:01.927][biodb::testThat]
biodb.TRACE[2024-03-27 20:36:01.946][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:36:01.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:36:01.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:01.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:01.951][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:36:01.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:36:01.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:01.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:01.955][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:36:01.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:36:01.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:01.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:01.959][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:36:01.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:36:01.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:01.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:02.004][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:36:02.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:36:02.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:02.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:02.009][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:36:02.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:36:02.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:02.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:02.013][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:36:02.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:36:02.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:02.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:02.017][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:36:02.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:36:02.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:02.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:36:02.032][biodb::testThat]
biodb.INFO [2024-03-27 20:36:02.034][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-27 20:36:02.035][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:36:02.037][biodb::testThat]
biodb.INFO [2024-03-27 20:36:02.050][biodb::testThat]
biodb.INFO [2024-03-27 20:36:02.051][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-27 20:36:02.052][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:36:02.053][biodb::testThat]
biodb.INFO [2024-03-27 20:36:02.062][biodb::testThat]
biodb.INFO [2024-03-27 20:36:02.063][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-27 20:36:02.064][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:36:02.065][biodb::testThat]
biodb.DEBUG[2024-03-27 20:36:02.069][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-03-27 20:36:03.194][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-03-27 20:36:03.752][biodb::testThat]
biodb.INFO [2024-03-27 20:36:03.754][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-27 20:36:03.756][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:36:03.757][biodb::testThat]
biodb.TRACE[2024-03-27 20:36:03.765][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:03.767][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:03.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:03.769][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:03.770][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:03.772][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:03.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:03.774][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 20:36:03.777][biodb::testThat]
biodb.INFO [2024-03-27 20:36:03.778][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-03-27 20:36:03.779][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:36:03.780][biodb::testThat]
biodb.TRACE[2024-03-27 20:36:03.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:03.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:03.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:03.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:03.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:03.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:03.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:03.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:03.800][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:03.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:03.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:03.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:36:03.886][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 20:36:03.889][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:36:03.891][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-27 20:36:03.892][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:36:03.893][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-03-27 20:36:03.962][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-27 20:36:03.965][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:36:03.967][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-27 20:36:03.968][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:36:03.969][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-03-27 20:36:03.981][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 20:36:03.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 20:36:03.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:03.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:03.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:36:03.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:36:03.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:03.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:03.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:03.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:03.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:03.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:04.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:04.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:04.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:04.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:04.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:04.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:04.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:04.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:04.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:04.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:04.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:04.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:04.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:04.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:04.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:04.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:36:04.022][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-03-27 20:36:04.038][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:36:04.039][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:36:04.054][private$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[2024-03-27 20:36:08.043][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[2024-03-27 20:36:19.077][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:36:19.079][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-03-27 20:36:19.093][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-03-27 20:36:20.011][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[2024-03-27 20:36:20.014][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:36:20.015][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:36:20.017][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-03-27 20:36:20.695][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-03-27 20:36:21.386][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:36:21.391][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-03-27 20:36:21.400][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-03-27 20:36:21.441][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-03-27 20:36:21.446][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:36:21.448][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:36:21.451][private$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[2024-03-27 20:36:22.150][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[2024-03-27 20:36:22.850][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:36:22.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-03-27 20:36:22.863][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-03-27 20:36:22.895][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 20:36:22.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 20:36:22.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:22.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:36:22.912][biodb::testThat]
biodb.INFO [2024-03-27 20:36:22.914][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-03-27 20:36:22.915][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:36:22.916][biodb::testThat]
biodb.TRACE[2024-03-27 20:36:22.920][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 20:36:22.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 20:36:22.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:22.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:22.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:36:22.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:36:22.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:22.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:22.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:22.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:22.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:22.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:22.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:22.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:22.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:22.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:22.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:22.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:22.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:22.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:22.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:22.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:22.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:22.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:36:22.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:22.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:22.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:22.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:22.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:22.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:22.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:36:22.971][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[2024-03-27 20:36:22.975][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:36:22.976][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:36:23.009][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-03-27 20:36:27.303][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-03-27 20:36:38.367][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:36:38.369][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-03-27 20:36:38.383][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-03-27 20:36:39.246][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-03-27 20:36:39.292][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-27 20:36:39.294][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-03-27 20:36:39.295][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-27 20:36:39.296][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:36:39.297][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:36:39.298][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 20:36:39.299][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:36:39.300][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:36:39.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:39.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:39.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:39.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:39.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:39.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:39.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:36:39.326][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-03-27 20:36:39.328][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:36:39.329][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:36:39.331][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-27 20:36:40.026][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-03-27 20:36:40.734][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:36:40.739][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-03-27 20:36:40.745][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-03-27 20:36:40.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:40.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:40.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:40.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:40.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:40.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:40.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:36:40.768][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-03-27 20:36:40.773][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:36:40.774][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:36:40.777][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-03-27 20:36:41.484][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-03-27 20:36:42.177][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:36:42.182][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-03-27 20:36:42.189][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-03-27 20:36:42.205][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-03-27 20:36:42.209][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:36:42.212][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-27 20:36:42.215][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 20:36:42.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:42.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:42.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:42.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:42.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:42.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:42.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:36:42.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:36:42.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:36:42.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:36:42.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:36:42.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.296][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:36:42.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:36:42.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.300][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:36:42.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:36:42.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.304][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:36:42.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:36:42.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.308][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:36:42.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:36:42.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:36:42.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:36:42.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.316][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:36:42.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:36:42.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.320][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:36:42.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:42.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.324][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:36:42.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:42.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:36:42.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:36:42.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.332][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:36:42.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:36:42.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:42.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:42.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.344][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:36:42.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.348][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 20:36:42.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.352][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:42.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:42.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.360][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:36:42.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.363][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.367][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.375][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:36:42.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:42.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:42.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:42.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:42.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:42.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:42.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:36:42.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:36:42.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:36:42.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.426][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:36:42.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:36:42.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.429][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:36:42.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:36:42.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.433][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:36:42.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:36:42.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.437][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:36:42.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:36:42.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.440][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:36:42.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:36:42.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.444][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:36:42.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:36:42.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.448][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:36:42.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:42.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.451][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:36:42.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:42.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.455][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:36:42.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:36:42.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.458][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:36:42.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:36:42.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:42.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:42.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.469][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:36:42.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.473][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 20:36:42.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:42.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:36:42.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.484][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:36:42.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:36:42.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.487][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.491][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.498][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:36:42.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:36:42.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:36:42.534][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-03-27 20:36:42.553][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:36:42.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:42.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:42.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:42.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:42.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:42.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:42.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:36:42.564][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.567][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.571][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:42.572][private$selectFields]
biodb.TRACE[2024-03-27 20:36:42.573][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:36:42.574][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:36:42.574][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:42.575][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.576][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.578][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.579][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.580][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.582][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.582][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:42.583][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:42.584][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.585][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.587][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.588][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:36:42.589][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.592][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.596][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.608][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-27 20:36:42.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:42.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:42.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:42.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:42.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:42.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:42.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:36:42.618][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.622][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.625][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:42.626][private$selectFields]
biodb.TRACE[2024-03-27 20:36:42.627][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:36:42.628][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:36:42.629][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:42.629][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.630][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.632][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.633][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.634][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.636][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.636][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:42.637][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:42.638][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.639][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.641][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.642][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:36:42.643][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.646][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.650][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.654][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-27 20:36:42.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:42.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:42.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:42.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:42.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:42.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:42.663][FUN] Functions in observer BiodbConfig: [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[2024-03-27 20:36:42.664][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.668][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.671][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:42.681][private$selectFields]
biodb.TRACE[2024-03-27 20:36:42.682][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:36:42.683][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:36:42.684][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:42.685][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.686][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.688][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.689][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.689][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.691][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.692][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:42.693][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:42.694][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.695][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.696][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.697][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:36:42.698][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.702][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.705][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:42.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.709][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-27 20:36:42.710][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:36:42.711][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 20:36:42.719][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 20:36:42.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 20:36:42.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:36:42.726][biodb::testThat]
biodb.INFO [2024-03-27 20:36:42.727][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-03-27 20:36:42.727][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:36:42.728][biodb::testThat]
biodb.TRACE[2024-03-27 20:36:42.731][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 20:36:42.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 20:36:42.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:36:42.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:36:42.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:42.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:42.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:42.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:42.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:42.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:42.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:42.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:42.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:42.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:42.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:36:42.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:42.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:42.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:42.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:42.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:42.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:42.818][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[2024-03-27 20:36:42.821][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[2024-03-27 20:36:42.824][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:36:42.825][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:36:42.827][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-03-27 20:36:47.027][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-03-27 20:36:57.901][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:36:57.904][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-03-27 20:36:57.918][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-03-27 20:36:58.810][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:36:58.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:58.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:58.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:58.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:58.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:58.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:58.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:36:58.857][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.861][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.885][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:58.886][private$selectFields]
biodb.TRACE[2024-03-27 20:36:58.887][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:36:58.888][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:36:58.889][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:58.890][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.891][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.893][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.895][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.896][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.897][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.899][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:58.919][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:58.920][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.921][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.923][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.923][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:36:58.924][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.928][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.932][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.936][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-27 20:36:58.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:58.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:58.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:58.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:58.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:58.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:58.945][FUN] Functions in observer BiodbConfig: [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[2024-03-27 20:36:58.946][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.950][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.953][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:58.954][private$selectFields]
biodb.TRACE[2024-03-27 20:36:58.955][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:36:58.956][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:36:58.957][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:58.958][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.959][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.960][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.961][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.962][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.964][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.965][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:58.966][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:58.967][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.968][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.969][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.970][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:36:58.972][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.975][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.979][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.983][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-27 20:36:58.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:58.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:58.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:58.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:58.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:58.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:58.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:36:58.993][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:58.997][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:58.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:58.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:59.000][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:59.001][private$selectFields]
biodb.TRACE[2024-03-27 20:36:59.002][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:36:59.003][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:36:59.004][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:59.005][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:59.006][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:59.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.007][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:59.008][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:59.009][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:59.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.011][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:59.012][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:59.013][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:36:59.014][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:59.015][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:59.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.016][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:59.017][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:36:59.018][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:59.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:59.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:59.022][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:59.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:59.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:59.026][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:59.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:36:59.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:59.030][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-27 20:36:59.030][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:36:59.031][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 20:36:59.217][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 20:36:59.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 20:36:59.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:36:59.224][biodb::testThat]
biodb.INFO [2024-03-27 20:36:59.225][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-03-27 20:36:59.225][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:36:59.226][biodb::testThat]
biodb.TRACE[2024-03-27 20:36:59.229][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-27 20:36:59.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-27 20:36:59.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:59.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-27 20:36:59.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-27 20:36:59.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:59.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:59.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:59.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:59.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:59.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:59.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:59.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:59.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:59.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:36:59.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:59.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:36:59.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:36:59.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:36:59.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:36:59.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:36:59.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:36:59.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:36:59.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:36:59.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:36:59.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:36:59.265][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-03-27 20:36:59.267][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:36:59.269][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-03-27 20:36:59.270][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:36:59.314][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-03-27 20:37:00.117][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:37:00.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:37:00.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:37:00.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:37:00.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:37:00.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:37:00.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:37:00.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:37:00.129][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.132][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.136][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:37:00.137][private$selectFields]
biodb.TRACE[2024-03-27 20:37:00.138][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:37:00.139][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:37:00.139][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:37:00.140][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.141][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.143][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.144][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.145][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.147][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.148][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:37:00.148][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:37:00.149][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.150][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.152][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.153][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:37:00.154][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.157][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.161][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.165][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-27 20:37:00.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:37:00.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:37:00.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:37:00.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:37:00.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:37:00.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:37:00.179][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.TRACE[2024-03-27 20:37:00.181][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.186][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.190][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:37:00.191][private$selectFields]
biodb.TRACE[2024-03-27 20:37:00.192][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:37:00.193][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:37:00.194][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:37:00.195][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.196][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.198][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.199][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.200][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.202][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.203][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:37:00.205][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:37:00.206][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.207][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.209][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.210][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:37:00.211][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.215][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.219][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.223][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-27 20:37:00.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:37:00.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:37:00.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:37:00.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:37:00.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:37:00.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:37:00.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:37:00.236][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.241][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.245][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:37:00.246][private$selectFields]
biodb.TRACE[2024-03-27 20:37:00.247][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-27 20:37:00.248][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:37:00.249][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:37:00.250][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.251][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.253][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.254][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.255][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.257][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.258][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:37:00.259][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:37:00.260][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.262][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.290][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.291][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-27 20:37:00.292][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.296][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.300][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:00.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:00.304][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-27 20:37:00.305][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:37:00.306][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-27 20:37:00.323][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-27 20:37:00.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-27 20:37:00.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:00.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-27 20:37:00.330][biodb::testThat]
biodb.INFO [2024-03-27 20:37:00.331][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-03-27 20:37:00.332][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:37:00.333][biodb::testThat]
biodb.DEBUG[2024-03-27 20:37:00.335][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-03-27 20:37:00.336][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-27 20:37:00.337][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-03-27 20:37:00.339][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-27 20:37:00.340][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:37:00.341][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:37:00.342][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 20:37:00.343][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:37:00.344][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:37:00.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:37:00.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:37:00.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:37:00.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:37:00.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:37:00.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:37:00.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:37:00.367][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-03-27 20:37:00.370][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:00.371][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:00.372][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:37:01.041][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:01.042][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:01.043][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:01.044][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:37:01.754][private$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[2024-03-27 20:37:01.755][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:01.756][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:01.757][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:37:02.431][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:02.433][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:02.435][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:02.436][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:37:03.235][private$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[2024-03-27 20:37:03.237][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:03.238][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:03.240][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:37:03.935][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:03.936][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:03.937][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:03.938][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:37:04.732][private$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[2024-03-27 20:37:04.733][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:04.735][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:04.737][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:37:05.414][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:05.416][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:05.417][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:05.418][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:37:06.223][private$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[2024-03-27 20:37:06.224][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:06.225][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:06.227][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:37:06.919][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:06.920][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:06.921][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:06.922][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:37:07.731][private$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[2024-03-27 20:37:07.733][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:07.734][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:07.736][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:37:08.375][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:08.376][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:08.377][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:08.379][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:37:09.185][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:37:09.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:09.252][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:09.254][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:37:09.933][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:09.935][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:09.936][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:09.938][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:37:10.746][private$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[2024-03-27 20:37:10.749][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:10.751][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:10.754][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:37:11.408][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:11.409][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:11.410][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:11.411][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:37:12.174][private$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[2024-03-27 20:37:12.176][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:12.178][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:12.181][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:37:12.843][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:12.844][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:12.846][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:12.847][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:37:13.656][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:37:13.659][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:13.661][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:13.664][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-27 20:37:14.330][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:14.333][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:14.336][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:14.338][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-27 20:37:15.129][private$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[2024-03-27 20:37:15.132][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-03-27 20:37:15.134][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:37:15.135][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-27 20:37:15.137][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 20:37:15.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:37:15.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:37:15.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:37:15.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:37:15.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:37:15.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:37:15.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:37:15.151][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:15.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:15.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:15.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:15.155][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:15.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:15.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:15.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:15.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:15.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:15.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:15.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:15.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:15.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:15.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:15.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:15.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:15.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:15.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:15.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:15.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:15.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:15.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:15.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:15.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:15.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:15.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:15.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:15.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:15.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:15.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:15.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:37:15.183][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-03-27 20:37:15.184][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-03-27 20:37:15.192][biodb::testThat]
biodb.INFO [2024-03-27 20:37:15.193][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-03-27 20:37:15.194][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:37:15.195][biodb::testThat]
biodb.DEBUG[2024-03-27 20:37:15.202][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-03-27 20:37:15.204][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-03-27 20:37:15.205][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-27 20:37:15.206][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-03-27 20:37:15.208][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-27 20:37:15.209][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-27 20:37:15.210][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:37:15.211][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 20:37:15.212][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-27 20:37:15.213][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-27 20:37:15.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:37:15.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:37:15.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:37:15.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:37:15.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:37:15.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:37:15.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:37:15.228][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-03-27 20:37:15.231][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:15.232][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:15.233][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:37:15.859][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:15.860][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:15.861][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[2024-03-27 20:37:15.862][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:37:16.667][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:37:16.669][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:16.726][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:16.729][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:37:17.379][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:17.380][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:17.381][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[2024-03-27 20:37:17.382][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:37:18.184][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:37:18.186][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:18.187][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:18.189][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:37:18.835][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:18.836][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:18.837][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[2024-03-27 20:37:18.838][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:37:19.609][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:37:19.610][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:19.612][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:19.613][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:37:20.258][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:20.260][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:20.263][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[2024-03-27 20:37:20.265][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:37:21.033][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:37:21.035][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:21.038][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:21.041][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:37:21.681][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:21.684][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:21.686][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[2024-03-27 20:37:21.687][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:37:22.491][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:37:22.493][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:22.495][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:22.497][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:37:23.118][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:23.119][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:23.120][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[2024-03-27 20:37:23.122][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:37:23.890][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:37:23.891][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:23.892][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:23.893][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:37:24.542][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:24.543][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:24.544][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:24.545][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:37:25.310][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:37:25.311][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:25.312][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:25.314][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:37:25.934][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:25.935][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:25.936][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[2024-03-27 20:37:25.937][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:37:26.702][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:37:26.704][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:26.705][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:26.707][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:37:27.356][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:27.359][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:27.361][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[2024-03-27 20:37:27.364][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:37:28.172][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:37:28.175][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:28.177][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:28.180][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-27 20:37:28.803][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:28.806][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:28.809][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[2024-03-27 20:37:28.812][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-27 20:37:29.579][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-27 20:37:29.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:37:29.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:37:29.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:37:29.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:37:29.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:37:29.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:37:29.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:37:29.611][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-03-27 20:37:29.618][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:29.620][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:29.627][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:37:30.270][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:30.272][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:30.275][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:30.277][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:37:31.087][private$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[2024-03-27 20:37:31.090][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:31.092][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:31.095][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:37:31.733][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:31.735][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:31.738][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:31.740][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:37:32.552][private$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[2024-03-27 20:37:32.555][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:32.557][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:32.560][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:37:33.220][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:33.223][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:33.225][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:33.228][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:37:34.034][private$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[2024-03-27 20:37:34.035][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:34.037][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:34.038][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:37:34.688][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:34.689][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:34.691][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:34.692][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:37:35.457][private$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[2024-03-27 20:37:35.458][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:35.459][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:35.461][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:37:36.081][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:36.083][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:36.085][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:36.087][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:37:36.895][private$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[2024-03-27 20:37:36.898][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:36.990][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:36.992][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:37:37.613][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:37.614][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:37.615][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:37.616][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:37:38.324][private$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[2024-03-27 20:37:38.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:38.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:38.328][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:37:38.947][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:38.949][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:38.951][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:38.953][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:37:39.760][private$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[2024-03-27 20:37:39.762][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:39.763][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:39.764][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:37:40.456][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:40.457][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:40.458][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:40.461][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:37:41.269][private$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[2024-03-27 20:37:41.272][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:41.274][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:41.277][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:37:41.927][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:41.930][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:41.932][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:41.935][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:37:42.746][private$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[2024-03-27 20:37:42.749][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:42.751][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:42.754][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-27 20:37:43.424][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-27 20:37:43.425][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-27 20:37:43.426][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-27 20:37:43.427][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-27 20:37:44.245][private$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[2024-03-27 20:37:44.254][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-03-27 20:37:44.258][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-27 20:37:44.261][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-27 20:37:44.265][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 20:37:44.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:37:44.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:37:44.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:37:44.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:37:44.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:37:44.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:37:44.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:37:44.296][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:44.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:44.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.302][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:44.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:44.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:44.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:44.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:37:44.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:37:44.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:37:44.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:37:44.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:37:44.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:37:44.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:37:44.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:37:44.327][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:44.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:44.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.331][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:44.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:37:44.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:44.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:44.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:44.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:44.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:44.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:44.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:44.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:44.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:44.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:44.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:44.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:44.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:44.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:44.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:44.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:44.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:44.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:44.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:44.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:44.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:37:44.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:37:44.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:37:44.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:37:44.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:37:44.380][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-03-27 20:37:44.381][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-27 20:37:44.413][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-03-27 20:37:44.558][biodb::testThat]
biodb.INFO [2024-03-27 20:37:44.559][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-03-27 20:37:44.560][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:37:44.560][biodb::testThat]
biodb.INFO [2024-03-27 20:37:44.617][biodb::testThat]
biodb.INFO [2024-03-27 20:37:44.618][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-03-27 20:37:44.619][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:37:44.620][biodb::testThat]
biodb.INFO [2024-03-27 20:37:44.627][biodb::testThat]
biodb.INFO [2024-03-27 20:37:44.628][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-03-27 20:37:44.629][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:37:44.630][biodb::testThat]
biodb.DEBUG[2024-03-27 20:37:44.632][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[2024-03-27 20:37:44.635][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:37:44.636][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:37:44.638][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-03-27 20:37:48.755][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-03-27 20:37:59.707][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:37:59.710][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-03-27 20:37:59.724][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-03-27 20:38:00.607][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:00.609][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:00.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:00.611][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:00.612][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:00.613][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:00.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:00.615][ef$get] fields variable is a list.
biodb.INFO [2024-03-27 20:38:00.617][biodb::testThat]
biodb.INFO [2024-03-27 20:38:00.618][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-03-27 20:38:00.619][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:38:00.620][biodb::testThat]
biodb.ERROR[2024-03-27 20:38:00.635][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-03-27 20:38:00.653][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-03-27 20:38:00.666][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 20:38:00.667][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-27 20:38:00.668][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-27 20:38:00.669][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 20:38:00.670][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:00.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:00.672][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.674][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 20:38:00.685][biodb::testContext]
biodb.INFO [2024-03-27 20:38:00.686][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:38:00.687][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-03-27 20:38:00.688][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:38:00.689][biodb::testContext]
biodb.INFO [2024-03-27 20:38:00.691][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-27 20:38:00.692][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 20:38:00.697][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:38:00.698][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 20:38:00.699][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 20:38:00.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.701][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[2024-03-27 20:38:00.702][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 20:38:00.704][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 20:38:00.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.733][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 20:38:00.734][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 20:38:00.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.737][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 20:38:00.738][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 20:38:00.739][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 20:38:00.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.742][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 20:38:00.743][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 20:38:00.744][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 20:38:00.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.748][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 20:38:00.749][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 20:38:00.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.752][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 20:38:00.753][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 20:38:00.754][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 20:38:00.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.757][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 20:38:00.758][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 20:38:00.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.761][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 20:38:00.762][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 20:38:00.763][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 20:38:00.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.767][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:38:00.768][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 20:38:00.769][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 20:38:00.769][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 20:38:00.770][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 20:38:00.771][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 20:38:00.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.775][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 20:38:00.776][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 20:38:00.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.779][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 20:38:00.780][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 20:38:00.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.783][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 20:38:00.784][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 20:38:00.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.788][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 20:38:00.789][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 20:38:00.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.792][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 20:38:00.793][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 20:38:00.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.796][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:38:00.797][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 20:38:00.801][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 20:38:00.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.804][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 20:38:00.805][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 20:38:00.806][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 20:38:00.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.809][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[2024-03-27 20:38:00.810][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 20:38:00.812][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:00.813][self$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[2024-03-27 20:38:00.813][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.814][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:38:00.815][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.816][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:38:00.817][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:00.818][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:38:00.819][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:38:00.820][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:38:00.821][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.822][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 20:38:00.823][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:38:00.824][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.825][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.826][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:38:00.826][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:38:00.826][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:38:00.826][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:38:00.826][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:38:00.827][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:38:00.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:00.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:00.838][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:38:00.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:00.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:00.841][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:38:00.842][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.843][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:38:00.843][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:38:00.844][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:00.845][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.846][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 20:38:00.848][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:00.849][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:38:00.850][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.851][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:38:00.852][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.853][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:38:00.853][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:00.854][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:38:00.855][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:38:00.856][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:38:00.857][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.858][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 20:38:00.859][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:38:00.860][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.861][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.862][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:38:00.862][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:38:00.862][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:38:00.862][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:38:00.862][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:38:00.863][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:38:00.864][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:00.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:00.865][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:38:00.866][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:00.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:00.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:38:00.869][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.870][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:38:00.871][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:38:00.871][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:00.872][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.874][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 20:38:00.875][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.876][self$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[2024-03-27 20:38:00.877][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.878][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:38:00.879][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.880][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:38:00.881][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:00.882][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:38:00.883][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:38:00.884][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:38:00.885][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:00.885][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 20:38:00.886][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:38:00.887][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.888][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.889][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.890][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:38:00.891][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:00.892][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:00.893][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:38:00.894][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:00.894][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:00.895][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:38:00.896][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.897][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:38:00.898][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:38:00.899][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:00.900][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.901][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 20:38:00.902][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.903][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:38:00.904][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.905][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:38:00.906][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.907][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:38:00.908][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:00.909][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:38:00.910][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:38:00.911][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:38:00.912][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:00.912][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 20:38:00.913][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:38:00.914][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.915][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:00.916][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.917][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:38:00.918][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:00.919][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:00.920][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:38:00.921][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:00.921][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:00.922][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:38:00.923][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.924][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:38:00.925][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:38:00.926][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:00.927][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:00.928][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:38:00.929][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.988][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[2024-03-27 20:38:00.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.993][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[2024-03-27 20:38:00.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:00.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:00.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:00.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:00.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:00.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.005][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[2024-03-27 20:38:01.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.010][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 20:38:01.011][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 20:38:01.012][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 20:38:01.014][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 20:38:01.015][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:38:01.016][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 20:38:01.018][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 20:38:01.019][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 20:38:01.020][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 20:38:01.022][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 20:38:01.023][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:38:01.024][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 20:38:01.025][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 20:38:01.027][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 20:38:01.028][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 20:38:01.029][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:38:01.221][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 20:38:01.222][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 20:38:01.224][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:38:01.225][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 20:38:01.226][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 20:38:01.227][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 20:38:01.229][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 20:38:01.230][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 20:38:01.231][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 20:38:01.233][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 20:38:01.234][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 20:38:01.235][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 20:38:01.236][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 20:38:01.238][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 20:38:01.239][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 20:38:01.240][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 20:38:01.241][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 20:38:01.243][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 20:38:01.244][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 20:38:01.245][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 20:38:01.246][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 20:38:01.248][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 20:38:01.249][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 20:38:01.250][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 20:38:01.251][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 20:38:01.253][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 20:38:01.254][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 20:38:01.255][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 20:38:01.257][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 20:38:01.258][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 20:38:01.259][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 20:38:01.260][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 20:38:01.262][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 20:38:01.263][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 20:38:01.264][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 20:38:01.265][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 20:38:01.267][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 20:38:01.268][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 20:38:01.269][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 20:38:01.270][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 20:38:01.272][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 20:38:01.273][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 20:38:01.274][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 20:38:01.275][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 20:38:01.277][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 20:38:01.278][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 20:38:01.279][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 20:38:01.280][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 20:38:01.282][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 20:38:01.283][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 20:38:01.284][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:38:01.285][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:38:01.287][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 20:38:01.288][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 20:38:01.289][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 20:38:01.290][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 20:38:01.292][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 20:38:01.293][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 20:38:01.294][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 20:38:01.295][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 20:38:01.297][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 20:38:01.298][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 20:38:01.299][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 20:38:01.301][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 20:38:01.302][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 20:38:01.303][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 20:38:01.304][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 20:38:01.306][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 20:38:01.307][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-27 20:38:01.308][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:38:01.309][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.311][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.357][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[2024-03-27 20:38:01.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.375][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[2024-03-27 20:38:01.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.393][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[2024-03-27 20:38:01.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.399][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[2024-03-27 20:38:01.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:01.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:01.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:01.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:01.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:01.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:01.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:01.420][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-27 20:38:01.422][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:38:01.424][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:01.425][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 20:38:01.426][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:01.427][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:38:01.428][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:01.429][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:38:01.430][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:01.431][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:38:01.432][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:38:01.433][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:38:01.434][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:01.435][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-27 20:38:01.436][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:38:01.437][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-27 20:38:01.437][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-27 20:38:01.437][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-27 20:38:01.437][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-27 20:38:01.437][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-27 20:38:01.437][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-27 20:38:01.437][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-27 20:38:01.437][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-27 20:38:01.437][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-27 20:38:01.439][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:01.440][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:38:01.440][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:38:01.441][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:38:01.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:01.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:01.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:38:01.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:01.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:01.447][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:38:01.448][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 20:38:01.448][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-27 20:38:01.449][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:38:01.450][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:38:01.451][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:01.452][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:01.453][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-27 20:38:01.455][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:38:01.458][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:38:01.459][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-27 20:38:01.460][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:38:01.462][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-27 20:38:01.463][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 20:38:01.464][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 20:38:01.466][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-27 20:38:01.467][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-27 20:38:01.468][biodb::testThat]
biodb.INFO [2024-03-27 20:38:01.469][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-03-27 20:38:01.470][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:38:01.471][biodb::testThat]
biodb.DEBUG[2024-03-27 20:38:01.475][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-03-27 20:38:01.480][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:38:01.481][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:38:01.482][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-03-27 20:38:02.147][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[2024-03-27 20:38:02.839][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:38:02.842][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-03-27 20:38:02.845][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-03-27 20:38:02.862][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[2024-03-27 20:38:02.866][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:38:02.867][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:38:02.869][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-03-27 20:38:03.858][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-03-27 20:38:04.563][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:38:04.566][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-03-27 20:38:04.569][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-03-27 20:38:04.580][biodb::testThat]
biodb.INFO [2024-03-27 20:38:04.581][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-03-27 20:38:04.582][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:38:04.583][biodb::testThat]
biodb.INFO [2024-03-27 20:38:04.613][biodb::testThat]
biodb.INFO [2024-03-27 20:38:04.614][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-03-27 20:38:04.615][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:38:04.616][biodb::testThat]
biodb.DEBUG[2024-03-27 20:38:04.619][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-03-27 20:38:04.622][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:38:04.623][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:38:04.625][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-03-27 20:38:05.142][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-03-27 20:38:05.683][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:38:05.685][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-03-27 20:38:05.689][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-03-27 20:38:05.722][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[2024-03-27 20:38:05.725][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:38:05.727][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-03-27 20:38:05.728][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:38:05.729][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-03-27 20:38:05.736][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[2024-03-27 20:38:05.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:38:05.740][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:38:05.742][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-03-27 20:38:06.560][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-03-27 20:38:07.118][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:38:07.120][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-03-27 20:38:07.124][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-03-27 20:38:07.131][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-03-27 20:38:07.134][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:38:07.135][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:38:07.136][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-03-27 20:38:08.436][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-03-27 20:38:11.511][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:38:11.513][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-03-27 20:38:11.518][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-03-27 20:38:11.634][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[2024-03-27 20:38:11.637][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-27 20:38:11.638][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-27 20:38:11.640][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-03-27 20:38:13.255][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-03-27 20:38:16.664][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-27 20:38:16.667][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-03-27 20:38:16.673][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-03-27 20:38:16.790][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 20:38:16.792][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-27 20:38:16.793][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-27 20:38:16.794][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 20:38:16.795][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:16.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:16.797][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:16.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:16.798][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-27 20:38:16.803][biodb::testContext]
biodb.INFO [2024-03-27 20:38:16.804][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:38:16.805][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-03-27 20:38:16.806][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-27 20:38:16.807][biodb::testContext]
biodb.INFO [2024-03-27 20:38:16.810][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-27 20:38:16.811][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-03-27 20:38:16.816][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:38:16.817][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-27 20:38:16.818][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-27 20:38:16.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.821][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-27 20:38:16.822][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-27 20:38:16.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.826][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-27 20:38:16.827][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-27 20:38:16.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.831][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-27 20:38:16.832][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-27 20:38:16.833][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-27 20:38:16.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.837][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-27 20:38:16.838][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-27 20:38:16.839][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-27 20:38:16.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.843][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-27 20:38:16.844][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-27 20:38:16.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.847][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-27 20:38:16.848][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-27 20:38:16.849][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-27 20:38:16.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.853][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-27 20:38:16.854][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-27 20:38:16.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.858][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-27 20:38:16.859][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-27 20:38:16.860][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-27 20:38:16.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.863][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:38:16.864][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-27 20:38:16.865][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-27 20:38:16.866][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-27 20:38:16.867][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-27 20:38:16.868][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-27 20:38:16.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.872][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-27 20:38:16.873][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-27 20:38:16.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.877][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-27 20:38:16.878][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-27 20:38:16.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.881][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-27 20:38:16.882][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-27 20:38:16.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.886][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-27 20:38:16.887][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-27 20:38:16.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.890][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-27 20:38:16.892][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-27 20:38:16.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.895][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-27 20:38:16.896][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-27 20:38:16.900][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-27 20:38:16.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.903][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-27 20:38:16.904][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-27 20:38:16.905][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-27 20:38:16.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:16.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:16.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:16.909][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-27 20:38:16.911][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:16.912][self$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[2024-03-27 20:38:16.913][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:16.914][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:38:16.915][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:16.916][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:38:16.917][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:16.918][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:38:16.919][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:38:16.920][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:38:16.921][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:16.922][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-27 20:38:16.923][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:38:16.924][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:16.925][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:16.926][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:38:16.926][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:38:16.926][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:38:16.926][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:38:16.926][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:38:16.927][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:38:16.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:16.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:16.930][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:38:16.931][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:16.932][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:16.933][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:38:16.934][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:16.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:38:16.935][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:38:16.936][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:16.937][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:16.939][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-27 20:38:16.940][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:16.941][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:38:16.942][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:16.943][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:38:16.944][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:16.945][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:38:16.946][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:16.947][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:38:16.948][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:38:16.949][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:38:16.950][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:16.951][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-27 20:38:16.952][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:38:16.953][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:16.954][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:16.955][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:38:16.955][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:38:16.955][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-27 20:38:16.955][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-27 20:38:16.955][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-27 20:38:16.956][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:38:16.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:16.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:16.959][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:38:16.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:16.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:16.962][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:38:16.963][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:16.964][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:38:16.965][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:38:16.966][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:16.967][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:16.968][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-27 20:38:16.970][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:16.971][self$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[2024-03-27 20:38:16.972][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:16.973][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:38:16.975][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:16.976][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:38:16.977][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:16.978][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:38:16.979][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:38:16.980][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:38:16.982][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:16.983][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-27 20:38:16.984][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:38:16.985][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:16.986][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:16.987][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:16.988][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:38:16.988][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:16.989][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:16.990][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:38:16.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:16.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:16.993][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:38:16.994][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:16.995][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:38:16.996][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:38:16.997][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:16.998][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:16.999][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-27 20:38:17.001][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:17.002][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-27 20:38:17.003][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:17.004][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:38:17.005][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:17.006][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:38:17.007][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:17.008][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:38:17.009][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-27 20:38:17.010][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:38:17.011][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:17.012][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-27 20:38:17.013][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:38:17.014][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:17.015][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:17.016][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:17.017][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:38:17.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:17.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:17.020][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:38:17.021][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:17.022][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:17.023][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:38:17.024][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:17.025][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:38:17.026][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:38:17.027][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:17.028][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:17.029][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:38:17.030][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.071][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[2024-03-27 20:38:17.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.076][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[2024-03-27 20:38:17.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.080][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[2024-03-27 20:38:17.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.139][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-27 20:38:17.141][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-27 20:38:17.142][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-27 20:38:17.144][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-27 20:38:17.145][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-27 20:38:17.147][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-27 20:38:17.148][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-27 20:38:17.149][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-27 20:38:17.151][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-27 20:38:17.152][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-27 20:38:17.154][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-27 20:38:17.155][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-27 20:38:17.156][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-27 20:38:17.158][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-27 20:38:17.159][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-27 20:38:17.161][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:38:17.162][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-27 20:38:17.163][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-27 20:38:17.165][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-27 20:38:17.166][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-27 20:38:17.168][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-27 20:38:17.169][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-27 20:38:17.170][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-27 20:38:17.172][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-27 20:38:17.173][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-27 20:38:17.174][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-27 20:38:17.175][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-27 20:38:17.177][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-27 20:38:17.178][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-27 20:38:17.179][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-27 20:38:17.181][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-27 20:38:17.182][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-27 20:38:17.183][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-27 20:38:17.184][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-27 20:38:17.186][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-27 20:38:17.187][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-27 20:38:17.188][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-27 20:38:17.189][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-27 20:38:17.191][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-27 20:38:17.192][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-27 20:38:17.193][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-27 20:38:17.194][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-27 20:38:17.196][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-27 20:38:17.197][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-27 20:38:17.198][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-27 20:38:17.200][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-27 20:38:17.201][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-27 20:38:17.202][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-27 20:38:17.203][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-27 20:38:17.205][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-27 20:38:17.206][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-27 20:38:17.207][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-27 20:38:17.208][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-27 20:38:17.210][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-27 20:38:17.211][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-27 20:38:17.212][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-27 20:38:17.214][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-27 20:38:17.215][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-27 20:38:17.216][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-27 20:38:17.218][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-27 20:38:17.219][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-27 20:38:17.220][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-27 20:38:17.221][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-27 20:38:17.223][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-27 20:38:17.224][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-27 20:38:17.225][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-27 20:38:17.226][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-27 20:38:17.228][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-27 20:38:17.229][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-27 20:38:17.230][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-27 20:38:17.232][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-27 20:38:17.233][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-27 20:38:17.234][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-27 20:38:17.235][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-27 20:38:17.237][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-27 20:38:17.238][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-27 20:38:17.239][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-27 20:38:17.241][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-27 20:38:17.242][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-27 20:38:17.243][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-27 20:38:17.244][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-27 20:38:17.246][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-27 20:38:17.247][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-27 20:38:17.248][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-27 20:38:17.250][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-27 20:38:17.251][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-27 20:38:17.252][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.253][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-27 20:38:17.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:17.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:17.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:17.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:17.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:17.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-27 20:38:17.353][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-27 20:38:17.354][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:38:17.356][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:17.357][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-27 20:38:17.358][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:17.359][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-27 20:38:17.360][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:17.361][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-27 20:38:17.362][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:17.363][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-27 20:38:17.363][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-27 20:38:17.364][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-27 20:38:17.365][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:17.366][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-27 20:38:17.367][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-27 20:38:17.368][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-27 20:38:17.368][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-27 20:38:17.368][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-27 20:38:17.368][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-27 20:38:17.368][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-27 20:38:17.368][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-27 20:38:17.368][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-27 20:38:17.368][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-27 20:38:17.368][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-27 20:38:17.369][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-27 20:38:17.370][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-27 20:38:17.370][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-27 20:38:17.371][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-27 20:38:17.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:17.373][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:17.374][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-27 20:38:17.374][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-27 20:38:17.375][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-27 20:38:17.376][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-27 20:38:17.377][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-27 20:38:17.377][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-27 20:38:17.378][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-27 20:38:17.379][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-27 20:38:17.380][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-27 20:38:17.381][self$setPropertyValue]
biodb.DEBUG[2024-03-27 20:38:17.382][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-27 20:38:17.383][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-27 20:38:17.386][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:38:17.387][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-27 20:38:17.388][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-27 20:38:17.390][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-27 20:38:17.391][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 20:38:17.392][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-27 20:38:17.393][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-27 20:38:17.394][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-27 20:38:17.395][biodb::testThat]
biodb.INFO [2024-03-27 20:38:17.396][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-03-27 20:38:17.397][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-27 20:38:17.398][biodb::testThat]
biodb.DEBUG[2024-03-27 20:38:17.401][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-03-27 20:38:17.405][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-27 20:38:17.407][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-03-27 20:38:17.408][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-27 20:38:17.457][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-03-27 20:38:18.333][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-03-27 20:38:18.334][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-27 20:38:18.336][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-03-27 20:38:18.338][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-03-27 20:38:18.339][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-03-27 20:38:18.340][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-27 20:38:18.341][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-27 20:38:18.343][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-27 20:38:18.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:38:18.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:18.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:18.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:18.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:18.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:18.354][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[2024-03-27 20:38:18.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.376][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:38:18.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:38:18.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.380][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:38:18.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:38:18.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.384][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.388][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.392][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.396][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.400][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:38:18.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.404][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:38:18.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.408][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:18.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:18.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.412][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:18.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:18.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.420][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.424][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:38:18.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.428][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 20:38:18.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.436][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.441][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:38:18.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.463][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.471][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.483][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.487][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.495][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:38:18.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:38:18.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:18.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:18.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:18.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:18.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:18.520][FUN] Functions in observer BiodbConfig: [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[2024-03-27 20:38:18.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.541][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:38:18.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-27 20:38:18.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.545][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:38:18.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-27 20:38:18.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.549][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.553][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.557][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.561][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.565][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:38:18.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.569][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-27 20:38:18.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.573][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:18.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:18.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.577][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:18.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:18.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.589][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:38:18.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.593][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-27 20:38:18.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.597][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.600][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.604][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-27 20:38:18.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.608][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.612][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.620][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-27 20:38:18.658][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-03-27 20:38:18.661][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-27 20:38:18.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:38:18.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:18.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:18.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:18.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:18.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:18.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-27 20:38:18.689][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:38:18.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:38:18.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.692][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:38:18.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:38:18.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.696][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:38:18.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:38:18.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.700][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:38:18.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:38:18.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.703][private$selectFields] Fields none
biodb.TRACE[2024-03-27 20:38:18.704][private$selectFields]
biodb.TRACE[2024-03-27 20:38:18.705][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-03-27 20:38:18.706][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:38:18.707][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:38:18.708][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.709][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.711][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.711][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.712][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.714][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.715][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.716][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.718][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.719][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.720][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.722][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.723][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.724][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.725][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.726][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:18.727][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:18.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.729][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.730][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.731][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.733][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.733][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.734][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.736][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.737][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.738][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.740][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.741][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.742][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.743][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.744][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.745][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.747][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.748][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.749][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.751][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.752][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.753][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.754][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.755][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:18.756][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:18.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.758][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.759][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.760][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.762][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.762][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.763][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.765][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.766][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:38:18.767][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:38:18.768][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.769][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.771][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.772][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.773][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.774][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.775][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.776][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.778][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.779][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.780][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.782][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.783][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.784][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.786][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.786][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:18.787][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:18.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.789][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.790][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.791][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.793][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.794][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.795][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.797][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.798][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-03-27 20:38:18.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.822][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.825][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.829][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.833][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.837][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.841][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.856][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:18.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:18.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.860][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:18.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:18.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.863][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:18.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:18.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.879][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.882][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.886][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.896][private$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[2024-03-27 20:38:18.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-27 20:38:18.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:18.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:18.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:18.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:18.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:18.905][FUN] Functions in observer BiodbConfig: [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[2024-03-27 20:38:18.907][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:38:18.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:38:18.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.911][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-27 20:38:18.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-27 20:38:18.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.915][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-27 20:38:18.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-27 20:38:18.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.918][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-27 20:38:18.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-27 20:38:18.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.922][private$selectFields] Fields none
biodb.TRACE[2024-03-27 20:38:18.923][private$selectFields]
biodb.TRACE[2024-03-27 20:38:18.924][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-03-27 20:38:18.925][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-27 20:38:18.926][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:38:18.927][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.928][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.930][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.930][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.931][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.933][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.934][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.935][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.937][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.938][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.939][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.941][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.942][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.943][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.944][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.945][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:18.946][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:18.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.948][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.949][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.950][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.952][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.953][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.954][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.956][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.957][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.958][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.959][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.960][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.961][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.963][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.964][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.965][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:18.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.967][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.968][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.969][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:18.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.970][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.971][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.972][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:18.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.974][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.975][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:18.976][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:18.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.978][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.979][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:18.980][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:18.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.981][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.982][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.983][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:18.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.985][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.986][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:38:18.987][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-27 20:38:18.988][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:18.989][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:18.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:18.991][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:18.992][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.993][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:18.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.007][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.008][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:19.009][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:19.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.011][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.012][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:19.013][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:19.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.014][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.015][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:19.016][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:19.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.018][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.019][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:19.020][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:19.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.022][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.023][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:19.024][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:19.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.025][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.026][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:19.027][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:19.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.029][ef$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.030][private$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[2024-03-27 20:38:19.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:19.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:19.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:19.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:19.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-27 20:38:19.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-27 20:38:19.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:19.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:19.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:19.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:19.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-27 20:38:19.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-27 20:38:19.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.053][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:19.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:19.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.057][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:19.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:19.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.060][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:19.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-27 20:38:19.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.064][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:19.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:19.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.068][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:19.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:19.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.072][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:19.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-27 20:38:19.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:19.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:19.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:19.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:19.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:19.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-27 20:38:19.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.087][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:19.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:19.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.091][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:19.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:19.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.094][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-27 20:38:19.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-27 20:38:19.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:19.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:19.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:19.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:19.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-27 20:38:19.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-27 20:38:19.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.110][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:19.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:19.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.113][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:19.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:19.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.117][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:19.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-27 20:38:19.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-27 20:38:19.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-27 20:38:19.124][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-03-27 20:38:19.125][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-03-27 20:38:19.126][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-03-27 20:38:19.132][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-27 20:38:19.133][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-27 20:38:19.134][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-27 20:38:19.135][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-27 20:38:19.135][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-27 20:38:19.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-27 20:38:19.137][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-27 20:38:19.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-27 20:38:19.139][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-27 20:38:19.140][FUN] Functions in observer 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
LipidmapsStructureConn0.8920.1163.215
LipidmapsStructureEntry0.1620.0050.165