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This page was generated on 2024-04-17 11:35:48 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_18
git_last_commit: f02eedd
git_last_commit_date: 2023-10-24 11:38:15 -0400 (Tue, 24 Oct 2023)
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: 2024-04-15 20:33:54 -0400 (Mon, 15 Apr 2024)
EndedAt: 2024-04-15 20:39:15 -0400 (Mon, 15 Apr 2024)
EllapsedTime: 320.9 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
 OK
* 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 [2024-04-15 20:34:45.034][biodb::testContext]
biodb.INFO [2024-04-15 20:34:45.037][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 20:34:45.038][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-04-15 20:34:45.039][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 20:34:45.040][biodb::testContext]
biodb.INFO [2024-04-15 20:34:45.054][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 20:34:45.059][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 20:34:45.075][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 20:34:45.077][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 20:34:45.080][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 20:34:45.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.089][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 20:34:45.118][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 20:34:45.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.125][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[2024-04-15 20:34:45.127][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 20:34:45.129][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 20:34:45.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.134][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 20:34:45.136][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 20:34:45.138][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 20:34:45.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.145][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 20:34:45.147][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 20:34:45.149][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 20:34:45.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.156][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 20:34:45.158][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 20:34:45.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.166][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 20:34:45.168][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 20:34:45.170][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 20:34:45.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.177][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 20:34:45.179][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 20:34:45.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.187][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 20:34:45.189][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 20:34:45.191][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 20:34:45.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.197][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 20:34:45.198][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 20:34:45.199][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 20:34:45.200][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 20:34:45.201][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 20:34:45.203][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 20:34:45.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.209][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 20:34:45.211][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 20:34:45.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.215][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 20:34:45.217][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 20:34:45.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.221][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 20:34:45.222][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 20:34:45.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.229][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 20:34:45.231][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 20:34:45.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.238][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 20:34:45.240][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 20:34:45.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.248][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 20:34:45.250][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 20:34:45.256][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 20:34:45.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.260][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[2024-04-15 20:34:45.261][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 20:34:45.262][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 20:34:45.264][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 20:34:45.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.271][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 20:34:45.327][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:45.370][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 20:34:45.372][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.374][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:34:45.376][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.377][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:34:45.379][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:45.381][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:34:45.383][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 20:34:45.385][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:34:45.387][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.389][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 20:34:45.391][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:34:45.392][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.394][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.396][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 20:34:45.396][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 20:34:45.396][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 20:34:45.396][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 20:34:45.396][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 20:34:45.397][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:34:45.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:34:45.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:34:45.403][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:34:45.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:34:45.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:34:45.407][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:34:45.409][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.411][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:34:45.412][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:34:45.414][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:45.416][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.418][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 20:34:45.421][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:45.422][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 20:34:45.424][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.425][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:34:45.426][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.427][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:34:45.429][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:45.430][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:34:45.432][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 20:34:45.434][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:34:45.435][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.436][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 20:34:45.437][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:34:45.438][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.439][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.440][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 20:34:45.440][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 20:34:45.440][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 20:34:45.440][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 20:34:45.440][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 20:34:45.441][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:34:45.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:34:45.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:34:45.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:34:45.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:34:45.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:34:45.447][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:34:45.449][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.451][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:34:45.452][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:34:45.454][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:45.456][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.457][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 20:34:45.459][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.461][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 20:34:45.463][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.464][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:34:45.466][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.468][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:34:45.469][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:45.471][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:34:45.472][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 20:34:45.474][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:34:45.476][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:45.477][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 20:34:45.479][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:34:45.480][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.481][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.482][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.484][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:34:45.484][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:34:45.486][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:34:45.487][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:34:45.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:34:45.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:34:45.491][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:34:45.492][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.494][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:34:45.496][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:34:45.497][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:45.499][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.501][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 20:34:45.504][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.506][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 20:34:45.508][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.510][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:34:45.512][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.513][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:34:45.515][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:45.517][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:34:45.519][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 20:34:45.520][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:34:45.521][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:45.522][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 20:34:45.523][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:34:45.524][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.525][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:45.526][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.527][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:34:45.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:34:45.529][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:34:45.530][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:34:45.531][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:34:45.532][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:34:45.533][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:34:45.534][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.535][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:34:45.536][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:34:45.537][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:45.538][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:45.542][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 20:34:45.543][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.575][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[2024-04-15 20:34:45.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.599][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[2024-04-15 20:34:45.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.608][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[2024-04-15 20:34:45.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.645][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 20:34:45.655][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 20:34:45.658][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 20:34:45.662][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 20:34:45.665][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 20:34:45.668][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 20:34:45.670][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 20:34:45.673][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 20:34:45.677][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 20:34:45.680][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 20:34:45.683][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 20:34:45.684][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 20:34:45.686][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 20:34:45.687][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 20:34:45.689][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 20:34:45.690][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 20:34:45.691][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 20:34:45.693][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 20:34:45.694][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 20:34:45.696][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 20:34:45.697][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 20:34:45.699][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 20:34:45.700][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 20:34:45.703][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 20:34:45.704][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 20:34:45.706][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 20:34:45.708][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 20:34:45.709][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 20:34:45.711][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 20:34:45.714][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 20:34:45.716][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 20:34:45.718][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 20:34:45.719][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 20:34:45.733][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 20:34:45.736][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 20:34:45.740][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 20:34:45.743][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 20:34:45.746][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 20:34:45.749][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 20:34:45.751][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 20:34:45.753][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 20:34:45.756][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 20:34:45.759][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 20:34:45.761][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 20:34:45.763][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 20:34:45.764][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 20:34:45.766][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 20:34:45.767][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 20:34:45.769][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 20:34:45.770][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 20:34:45.772][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 20:34:45.774][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 20:34:45.777][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 20:34:45.779][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 20:34:45.782][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 20:34:45.784][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 20:34:45.787][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 20:34:45.789][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 20:34:45.792][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 20:34:45.795][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 20:34:45.797][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 20:34:45.801][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 20:34:45.803][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 20:34:45.805][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 20:34:45.807][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 20:34:45.809][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 20:34:45.810][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 20:34:45.812][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 20:34:45.814][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 20:34:45.816][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 20:34:45.818][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 20:34:45.821][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 20:34:45.823][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 20:34:45.825][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 20:34:45.828][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 20:34:45.830][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 20:34:45.833][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 20:34:45.835][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 20:34:45.838][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 20:34:45.841][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 20:34:45.843][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 20:34:45.846][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 20:34:45.848][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 20:34:45.859][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 20:34:45.862][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 20:34:45.868][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 20:34:45.870][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.872][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.885][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[2024-04-15 20:34:45.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.894][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[2024-04-15 20:34:45.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.972][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[2024-04-15 20:34:45.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:45.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:45.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:45.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:45.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:45.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:45.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:45.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:46.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:46.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:46.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:46.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:46.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:46.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:46.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:46.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:46.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:46.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:46.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:46.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:46.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:46.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:46.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:46.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:46.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:46.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:34:46.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:46.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:46.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:46.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:46.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:46.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:34:46.035][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-04-15 20:34:46.052][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 20:34:46.054][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:46.056][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 20:34:46.057][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:46.059][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:34:46.061][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:46.062][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:34:46.064][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:46.066][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:34:46.068][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 20:34:46.070][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:34:46.071][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:46.073][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-04-15 20:34:46.075][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:34:46.077][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-04-15 20:34:46.077][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-04-15 20:34:46.077][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-04-15 20:34:46.077][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-04-15 20:34:46.077][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-04-15 20:34:46.077][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-04-15 20:34:46.077][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-04-15 20:34:46.077][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-04-15 20:34:46.077][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-04-15 20:34:46.079][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 20:34:46.080][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 20:34:46.080][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 20:34:46.082][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:34:46.084][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:34:46.085][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:34:46.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:34:46.088][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:34:46.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:34:46.092][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:34:46.093][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 20:34:46.093][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-04-15 20:34:46.095][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:34:46.097][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:34:46.099][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 20:34:46.101][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:34:46.113][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-04-15 20:34:46.116][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 20:34:46.164][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 20:34:46.166][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-04-15 20:34:46.173][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 20:34:46.181][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-04-15 20:34:46.186][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 20:34:46.188][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 20:34:46.191][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-04-15 20:34:46.194][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-04-15 20:34:46.213][biodb::testThat]
biodb.INFO [2024-04-15 20:34:46.215][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-04-15 20:34:46.216][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:34:46.218][biodb::testThat]
biodb.TRACE[2024-04-15 20:34:46.225][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[2024-04-15 20:34:46.229][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-04-15 20:34:46.238][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 20:34:46.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:34:46.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:46.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:46.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:46.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:46.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:46.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:34:46.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:34:46.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:34:46.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.345][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 20:34:46.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 20:34:46.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.352][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 20:34:46.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 20:34:46.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.360][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:46.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:46.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.416][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:46.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:46.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.426][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:46.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:46.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.432][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:46.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:46.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.436][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 20:34:46.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:46.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.441][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 20:34:46.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:46.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.446][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:34:46.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:34:46.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.451][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:34:46.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:34:46.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.468][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 20:34:46.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.475][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-15 20:34:46.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.498][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 20:34:46.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.623][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.639][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.648][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.665][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:34:46.706][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-04-15 20:34:46.710][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 20:34:46.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 20:34:46.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.720][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 20:34:46.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 20:34:46.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.728][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-15 20:34:46.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-15 20:34:46.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.736][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-15 20:34:46.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-15 20:34:46.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.798][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.862][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.871][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.878][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:46.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.918][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.921][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.924][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:46.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:46.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.974][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:46.976][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:46.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:46.981][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:46.998][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.020][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.027][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.031][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.037][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.040][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.043][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.046][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.072][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:34:47.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:34:47.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.081][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:34:47.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:34:47.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.090][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:34:47.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:34:47.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.098][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:34:47.100][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:34:47.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.104][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.106][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:34:47.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:34:47.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.143][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.146][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.148][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.165][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.174][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.183][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.192][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.194][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.197][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.198][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.217][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:47.220][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:47.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.225][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.234][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.236][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.238][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.249][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:34:47.252][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:34:47.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.257][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.268][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.270][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.273][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.282][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.284][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.287][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.294][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.297][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.302][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 20:34:47.312][biodb::testThat]
biodb.INFO [2024-04-15 20:34:47.313][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-04-15 20:34:47.314][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:34:47.315][biodb::testThat]
biodb.DEBUG[2024-04-15 20:34:47.341][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-04-15 20:34:47.357][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 20:34:47.366][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-04-15 20:34:47.369][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 20:34:47.374][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-04-15 20:34:47.376][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 20:34:47.473][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-04-15 20:34:47.476][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 20:34:47.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:34:47.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:34:47.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:34:47.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:34:47.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:34:47.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:34:47.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:34:47.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:47.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:47.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:47.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:47.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:34:47.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:34:47.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:34:47.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:34:47.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.534][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 20:34:47.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 20:34:47.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.538][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 20:34:47.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 20:34:47.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.543][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.548][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:34:47.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.556][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:34:47.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.572][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 20:34:47.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.580][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 20:34:47.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:47.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.588][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:34:47.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:34:47.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.596][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:34:47.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:34:47.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.619][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 20:34:47.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.625][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-15 20:34:47.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.641][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 20:34:47.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.654][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.683][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:47.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:47.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.689][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:47.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:47.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:47.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:47.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.705][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:47.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:34:47.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:47.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:47.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:47.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:47.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:47.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:47.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:47.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:47.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:47.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:47.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:34:47.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:34:47.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:34:47.747][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-04-15 20:34:47.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-15 20:34:47.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-15 20:34:47.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-15 20:34:47.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-15 20:34:47.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-15 20:34:47.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-15 20:34:47.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-15 20:34:47.777][biodb::testThat]
biodb.INFO [2024-04-15 20:34:47.780][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-04-15 20:34:47.782][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:34:47.784][biodb::testThat]
biodb.TRACE[2024-04-15 20:34:47.791][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.793][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.797][ef$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:34:47.799][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-04-15 20:34:47.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:47.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:47.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:47.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:47.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:34:47.880][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-04-15 20:34:47.887][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-04-15 20:34:47.927][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:34:47.930][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:34:47.933][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-04-15 20:34:49.157][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-04-15 20:34:49.888][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:34:49.893][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-04-15 20:34:49.923][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-04-15 20:34:49.928][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-04-15 20:34:49.992][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:49.994][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:49.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:49.998][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 20:34:50.006][biodb::testThat]
biodb.INFO [2024-04-15 20:34:50.008][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-04-15 20:34:50.010][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:34:50.012][biodb::testThat]
biodb.TRACE[2024-04-15 20:34:50.057][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:50.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:50.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:50.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:50.065][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:50.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:50.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:50.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:50.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:50.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:50.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:50.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:34:50.273][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-04-15 20:34:50.289][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 20:34:50.317][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-04-15 20:34:50.320][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 20:34:50.323][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-04-15 20:34:50.351][biodb::testThat]
biodb.INFO [2024-04-15 20:34:50.353][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-04-15 20:34:50.355][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:34:50.357][biodb::testThat]
biodb.TRACE[2024-04-15 20:34:50.392][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 20:34:50.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 20:34:50.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:50.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:50.401][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 20:34:50.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 20:34:50.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:50.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:50.407][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-15 20:34:50.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-15 20:34:50.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:50.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:50.412][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-15 20:34:50.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-15 20:34:50.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:50.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:50.489][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 20:34:50.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 20:34:50.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:50.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:50.497][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 20:34:50.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 20:34:50.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:50.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:50.505][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-15 20:34:50.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-15 20:34:50.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:50.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:50.512][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-15 20:34:50.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-15 20:34:50.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:50.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-15 20:34:50.527][biodb::testThat]
biodb.INFO [2024-04-15 20:34:50.529][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-04-15 20:34:50.531][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:34:50.532][biodb::testThat]
biodb.INFO [2024-04-15 20:34:50.546][biodb::testThat]
biodb.INFO [2024-04-15 20:34:50.548][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-04-15 20:34:50.550][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:34:50.552][biodb::testThat]
biodb.INFO [2024-04-15 20:34:50.565][biodb::testThat]
biodb.INFO [2024-04-15 20:34:50.567][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-04-15 20:34:50.569][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:34:50.571][biodb::testThat]
biodb.DEBUG[2024-04-15 20:34:50.578][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-04-15 20:34:51.739][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-04-15 20:34:52.330][biodb::testThat]
biodb.INFO [2024-04-15 20:34:52.332][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-04-15 20:34:52.333][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:34:52.335][biodb::testThat]
biodb.TRACE[2024-04-15 20:34:52.345][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:52.347][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:52.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:52.351][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:52.353][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:52.355][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:52.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:52.358][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 20:34:52.362][biodb::testThat]
biodb.INFO [2024-04-15 20:34:52.363][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-04-15 20:34:52.365][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:34:52.367][biodb::testThat]
biodb.TRACE[2024-04-15 20:34:52.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:52.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:52.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:52.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:52.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:52.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:52.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:52.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:52.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:34:52.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:34:52.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:52.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:34:52.552][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-04-15 20:34:52.558][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 20:34:52.561][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-04-15 20:34:52.564][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 20:34:52.567][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-04-15 20:34:52.689][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-04-15 20:34:52.694][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 20:34:52.697][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-04-15 20:34:52.700][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 20:34:52.703][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-04-15 20:34:52.726][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-15 20:34:52.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-15 20:34:52.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:52.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:52.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 20:34:52.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 20:34:52.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:52.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:52.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:52.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:52.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:52.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:52.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:52.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:52.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:52.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:52.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:52.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:52.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:52.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:52.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:52.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:52.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:52.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:34:52.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:52.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:34:52.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:34:52.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:34:52.805][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-04-15 20:34:52.835][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:34:52.837][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:34:52.865][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-04-15 20:34:56.955][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-04-15 20:35:08.556][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:35:08.559][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-04-15 20:35:08.574][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-04-15 20:35:09.514][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-04-15 20:35:09.518][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:09.519][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:09.521][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-04-15 20:35:10.208][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-04-15 20:35:10.885][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:35:10.888][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-04-15 20:35:10.892][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-04-15 20:35:10.913][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-04-15 20:35:10.917][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:10.918][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:10.920][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-04-15 20:35:11.598][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-04-15 20:35:12.303][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:35:12.306][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-04-15 20:35:12.313][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-04-15 20:35:12.340][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-15 20:35:12.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-15 20:35:12.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:12.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-15 20:35:12.358][biodb::testThat]
biodb.INFO [2024-04-15 20:35:12.359][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-04-15 20:35:12.361][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:35:12.362][biodb::testThat]
biodb.TRACE[2024-04-15 20:35:12.367][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-15 20:35:12.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-15 20:35:12.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:12.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:12.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 20:35:12.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 20:35:12.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:12.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:12.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:12.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:12.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:12.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:12.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:12.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:12.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:12.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:12.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:12.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:12.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:12.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:12.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:12.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:12.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:12.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:35:12.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:12.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:12.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:12.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:12.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:12.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:12.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:35:12.428][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-04-15 20:35:12.434][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:12.435][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:12.454][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-04-15 20:35:16.466][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-04-15 20:35:27.117][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:35:27.120][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-04-15 20:35:27.134][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-04-15 20:35:28.216][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-04-15 20:35:28.258][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-04-15 20:35:28.260][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-04-15 20:35:28.261][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-04-15 20:35:28.262][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 20:35:28.263][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 20:35:28.264][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 20:35:28.265][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 20:35:28.266][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 20:35:28.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:28.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:28.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:28.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:28.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:28.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:28.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:35:28.290][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-04-15 20:35:28.294][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:28.295][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:28.297][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-04-15 20:35:28.986][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-04-15 20:35:29.658][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:35:29.661][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-04-15 20:35:29.664][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-04-15 20:35:29.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:29.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:29.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:29.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:29.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:29.674][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:29.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:35:29.676][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-04-15 20:35:29.679][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:29.679][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:29.681][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-04-15 20:35:30.363][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-04-15 20:35:31.082][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:35:31.085][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-04-15 20:35:31.088][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-04-15 20:35:31.090][private$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[2024-04-15 20:35:31.092][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 20:35:31.093][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-04-15 20:35:31.094][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 20:35:31.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:31.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:31.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:31.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:31.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:31.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:31.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:35:31.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:35:31.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:35:31.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:35:31.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:35:31.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.133][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 20:35:31.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 20:35:31.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.137][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 20:35:31.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 20:35:31.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.141][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:35:31.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:35:31.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.145][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:35:31.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:35:31.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.149][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:35:31.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:35:31.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.153][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:35:31.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:35:31.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.157][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 20:35:31.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:31.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.161][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 20:35:31.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:31.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.165][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:35:31.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:35:31.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.169][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:35:31.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:35:31.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:35:31.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:35:31.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.181][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 20:35:31.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.185][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-15 20:35:31.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:35:31.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.193][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:35:31.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.197][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 20:35:31.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.201][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.206][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.214][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:35:31.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:31.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:31.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:31.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:31.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:31.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:31.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:35:31.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:35:31.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:35:31.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.260][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 20:35:31.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 20:35:31.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.264][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 20:35:31.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 20:35:31.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.269][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:35:31.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:35:31.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.273][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:35:31.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:35:31.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.279][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:35:31.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:35:31.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.283][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:35:31.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:35:31.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.287][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 20:35:31.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:31.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.292][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 20:35:31.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:31.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.296][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:35:31.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:35:31.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.301][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:35:31.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:35:31.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.305][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:35:31.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:35:31.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.314][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 20:35:31.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.318][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-15 20:35:31.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:35:31.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:35:31.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.353][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 20:35:31.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:35:31.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.358][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.362][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.371][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:35:31.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:35:31.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:35:31.413][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-04-15 20:35:31.424][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-15 20:35:31.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:31.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:31.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:31.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:31.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:31.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:31.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:35:31.439][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.444][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.448][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:31.449][private$selectFields]
biodb.TRACE[2024-04-15 20:35:31.450][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 20:35:31.451][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 20:35:31.452][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:31.453][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.454][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.456][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.457][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.458][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.460][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.461][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:31.462][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:31.463][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.464][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.466][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.467][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-15 20:35:31.469][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.473][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.477][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.492][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-04-15 20:35:31.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:31.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:31.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:31.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:31.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:31.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:31.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:35:31.505][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.509][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.513][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:31.514][private$selectFields]
biodb.TRACE[2024-04-15 20:35:31.515][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 20:35:31.516][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 20:35:31.517][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:31.518][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.519][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.521][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.522][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.524][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.525][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.527][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:31.528][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:31.529][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.530][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.532][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.533][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-15 20:35:31.534][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.538][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.542][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.547][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-04-15 20:35:31.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:31.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:31.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:31.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:31.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:31.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:31.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:35:31.560][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.564][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.568][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:31.569][private$selectFields]
biodb.TRACE[2024-04-15 20:35:31.570][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 20:35:31.571][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 20:35:31.572][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:31.573][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.575][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.577][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.578][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.579][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.581][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.582][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:31.583][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:31.584][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.585][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.587][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.588][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-15 20:35:31.589][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.593][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.597][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:31.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.602][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-04-15 20:35:31.603][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-15 20:35:31.604][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-15 20:35:31.614][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-15 20:35:31.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-15 20:35:31.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-15 20:35:31.623][biodb::testThat]
biodb.INFO [2024-04-15 20:35:31.624][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-04-15 20:35:31.625][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:35:31.626][biodb::testThat]
biodb.TRACE[2024-04-15 20:35:31.629][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-15 20:35:31.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-15 20:35:31.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 20:35:31.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 20:35:31.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:31.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:31.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:31.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:31.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:31.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:31.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:31.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:31.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:31.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:31.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:35:31.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:31.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:31.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:31.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:31.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:31.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:31.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:35:31.746][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-04-15 20:35:31.749][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:31.750][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:31.752][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-04-15 20:35:35.754][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-04-15 20:35:46.522][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:35:46.524][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-04-15 20:35:46.541][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-04-15 20:35:47.695][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-15 20:35:47.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:47.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:47.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:47.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:47.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:47.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:47.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:35:47.741][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.745][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.767][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:47.768][private$selectFields]
biodb.TRACE[2024-04-15 20:35:47.769][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 20:35:47.770][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 20:35:47.770][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:47.771][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.772][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.774][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.775][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.776][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.778][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.779][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:47.789][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:47.790][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.791][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.792][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.793][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-15 20:35:47.794][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.798][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.804][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.808][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-04-15 20:35:47.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:47.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:47.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:47.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:47.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:47.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:47.818][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.TRACE[2024-04-15 20:35:47.819][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.824][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.830][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:47.831][private$selectFields]
biodb.TRACE[2024-04-15 20:35:47.832][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 20:35:47.833][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 20:35:47.833][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:47.834][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.835][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.837][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.838][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.839][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.841][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.842][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:47.843][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:47.844][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.845][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.847][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.847][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-15 20:35:47.848][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.853][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.856][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.861][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-04-15 20:35:47.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:47.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:47.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:47.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:47.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:47.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:47.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:35:47.872][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.875][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.879][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:47.880][private$selectFields]
biodb.TRACE[2024-04-15 20:35:47.881][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 20:35:47.882][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 20:35:47.883][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:47.884][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.885][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.888][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.889][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.891][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.893][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.894][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:47.895][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:47.896][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.897][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.899][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.900][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-15 20:35:47.901][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.905][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.908][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:47.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.913][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-04-15 20:35:47.914][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-15 20:35:47.915][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-15 20:35:47.924][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-15 20:35:47.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-15 20:35:47.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-15 20:35:47.931][biodb::testThat]
biodb.INFO [2024-04-15 20:35:47.932][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-04-15 20:35:47.934][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:35:47.935][biodb::testThat]
biodb.TRACE[2024-04-15 20:35:47.939][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-15 20:35:47.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-15 20:35:47.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 20:35:47.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 20:35:47.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:47.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:47.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:47.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:47.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:47.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:47.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:47.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:47.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:35:47.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:47.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:35:47.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:47.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:47.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:47.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:47.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:47.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:47.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:35:47.977][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-04-15 20:35:47.980][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 20:35:47.981][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-04-15 20:35:47.983][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 20:35:48.029][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-04-15 20:35:49.151][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-15 20:35:49.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:49.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:49.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:49.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:49.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:49.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:49.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:35:49.163][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.166][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.170][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:49.171][private$selectFields]
biodb.TRACE[2024-04-15 20:35:49.172][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 20:35:49.173][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 20:35:49.174][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:49.175][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.176][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.177][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.178][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.179][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.181][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.182][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:49.183][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:49.184][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.185][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.187][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.188][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-15 20:35:49.189][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.192][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.196][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.200][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-04-15 20:35:49.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:49.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:49.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:49.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:49.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:49.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:49.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:35:49.211][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.215][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.219][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:49.219][private$selectFields]
biodb.TRACE[2024-04-15 20:35:49.220][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 20:35:49.221][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 20:35:49.222][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:49.223][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.224][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.226][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.227][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.228][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.229][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.231][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:49.232][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:49.233][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.234][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.236][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.237][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-15 20:35:49.238][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.241][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.245][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.249][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-04-15 20:35:49.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:49.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:49.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:49.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:49.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:49.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:49.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:35:49.260][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.265][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.269][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:49.270][private$selectFields]
biodb.TRACE[2024-04-15 20:35:49.271][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 20:35:49.272][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 20:35:49.273][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:49.274][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.275][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.276][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.277][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.278][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.280][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.281][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:49.282][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:35:49.283][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.284][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.286][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.287][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-04-15 20:35:49.288][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.291][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.295][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:35:49.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:35:49.299][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-04-15 20:35:49.300][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-15 20:35:49.301][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-15 20:35:49.318][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-15 20:35:49.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-15 20:35:49.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:35:49.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-15 20:35:49.325][biodb::testThat]
biodb.INFO [2024-04-15 20:35:49.326][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-04-15 20:35:49.327][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:35:49.328][biodb::testThat]
biodb.DEBUG[2024-04-15 20:35:49.330][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-04-15 20:35:49.331][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 20:35:49.333][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-04-15 20:35:49.335][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 20:35:49.337][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 20:35:49.338][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 20:35:49.339][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 20:35:49.340][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 20:35:49.341][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 20:35:49.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:35:49.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:35:49.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:35:49.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:35:49.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:35:49.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:35:49.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:35:49.364][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-04-15 20:35:49.367][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:49.368][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:49.369][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 20:35:50.051][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:35:50.052][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:35:50.053][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:35:50.054][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 20:35:50.845][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:35:50.846][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:50.847][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:50.849][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 20:35:51.497][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:35:51.501][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:35:51.504][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:35:51.506][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 20:35:52.516][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:35:52.517][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:52.518][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:52.520][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 20:35:53.205][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:35:53.207][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:35:53.209][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:35:53.212][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 20:35:53.928][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:35:53.931][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:53.932][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:53.935][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 20:35:54.644][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:35:54.647][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:35:54.649][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:35:54.651][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 20:35:55.430][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:35:55.432][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:55.433][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:55.435][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 20:35:56.097][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:35:56.098][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:35:56.100][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:35:56.101][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 20:35:56.807][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:35:56.809][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:56.810][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:56.811][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 20:35:57.493][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:35:57.494][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:35:57.495][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:35:57.496][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 20:35:58.345][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:35:58.348][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:58.350][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:58.353][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 20:35:59.058][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:35:59.060][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:35:59.062][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:35:59.064][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 20:35:59.881][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:35:59.883][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:35:59.884][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:35:59.885][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 20:36:00.511][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:00.512][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:00.513][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:00.514][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 20:36:01.282][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:01.283][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:01.284][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:01.286][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 20:36:01.905][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:01.907][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:01.909][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:01.910][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 20:36:02.620][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:02.623][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:02.625][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:02.627][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 20:36:03.256][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:03.257][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:03.258][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:03.259][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 20:36:04.046][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-04-15 20:36:04.049][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-04-15 20:36:04.051][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 20:36:04.053][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-04-15 20:36:04.054][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 20:36:04.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:36:04.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:04.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:04.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:04.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:04.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:04.067][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.TRACE[2024-04-15 20:36:04.069][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:36:04.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:36:04.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:04.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:04.073][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:36:04.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:36:04.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:04.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:04.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:04.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:04.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:04.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:04.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:04.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:04.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:04.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:04.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:04.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:04.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:04.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:04.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:04.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:04.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:04.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:04.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:04.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:04.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:04.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:04.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:04.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:04.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:04.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:36:04.157][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-04-15 20:36:04.158][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-04-15 20:36:04.166][biodb::testThat]
biodb.INFO [2024-04-15 20:36:04.167][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-04-15 20:36:04.168][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:36:04.169][biodb::testThat]
biodb.DEBUG[2024-04-15 20:36:04.176][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-04-15 20:36:04.177][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-04-15 20:36:04.178][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-04-15 20:36:04.180][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-04-15 20:36:04.181][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-04-15 20:36:04.182][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 20:36:04.183][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 20:36:04.184][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 20:36:04.185][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 20:36:04.186][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 20:36:04.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:36:04.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:04.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:04.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:04.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:04.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:04.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:04.201][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-04-15 20:36:04.203][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:04.204][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:04.206][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 20:36:04.837][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:04.839][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:04.840][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:04.842][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 20:36:05.644][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:05.646][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:05.647][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:05.649][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 20:36:06.305][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:06.306][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:06.307][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:06.308][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 20:36:07.016][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:07.017][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:07.019][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:07.020][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 20:36:07.657][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:07.658][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:07.660][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:07.661][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 20:36:08.439][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:08.440][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:08.441][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:08.443][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 20:36:09.092][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:09.095][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:09.097][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:09.098][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 20:36:09.803][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:09.804][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:09.805][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:09.807][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 20:36:10.422][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:10.423][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:10.424][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:10.425][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 20:36:11.188][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:11.189][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:11.190][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:11.191][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 20:36:11.813][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:11.815][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:11.816][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:11.817][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 20:36:12.580][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:12.581][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:12.582][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:12.584][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 20:36:13.269][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:13.271][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:13.273][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:13.275][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 20:36:13.984][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:13.986][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:13.989][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:13.992][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 20:36:14.693][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:14.695][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:14.698][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:14.701][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 20:36:15.507][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:15.508][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:15.509][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:15.510][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 20:36:16.132][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:16.135][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:16.137][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:16.140][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 20:36:16.945][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:16.946][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:16.947][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:16.949][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 20:36:17.567][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:17.568][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:17.570][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:17.571][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 20:36:18.338][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:18.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:36:18.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:18.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:18.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:18.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:18.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:18.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:18.370][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-04-15 20:36:18.377][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:18.379][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:18.382][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 20:36:19.029][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:19.033][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:19.035][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:19.038][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 20:36:19.881][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:19.884][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:19.886][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:19.890][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 20:36:20.546][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:20.548][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:20.551][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:20.553][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 20:36:21.364][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:21.367][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:21.369][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:21.373][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 20:36:22.029][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:22.031][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:22.033][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:22.036][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 20:36:22.742][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:22.743][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:22.745][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:22.746][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 20:36:23.367][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:23.369][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:23.372][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:23.375][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 20:36:24.183][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:24.186][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:24.188][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:24.191][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 20:36:24.859][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:24.862][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:24.864][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:24.867][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 20:36:25.673][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:25.674][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:25.675][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:25.677][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 20:36:26.299][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:26.300][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:26.302][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:26.303][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 20:36:27.066][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:27.067][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:27.068][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:27.070][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 20:36:27.685][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:27.686][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:27.687][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:27.688][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 20:36:28.447][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:28.449][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:28.450][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:28.451][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 20:36:29.067][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:29.069][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:29.070][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:29.071][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 20:36:29.832][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:29.835][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:29.837][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:29.841][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 20:36:30.498][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:30.500][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:30.501][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:30.502][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 20:36:31.265][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 20:36:31.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:31.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:31.269][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 20:36:31.889][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 20:36:31.890][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 20:36:31.891][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 20:36:31.893][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 20:36:32.599][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-04-15 20:36:32.603][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-04-15 20:36:32.604][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 20:36:32.606][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-04-15 20:36:32.607][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 20:36:32.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:36:32.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:32.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:32.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:32.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:32.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:32.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:36:32.623][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:36:32.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:36:32.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.628][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:36:32.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:36:32.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:32.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:32.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:36:32.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:36:32.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:32.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:32.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:32.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:32.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:32.646][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.TRACE[2024-04-15 20:36:32.648][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:36:32.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:36:32.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.652][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:36:32.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:36:32.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:32.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:32.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:32.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:32.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:32.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:32.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:32.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:32.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:32.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:32.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:32.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:32.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:32.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:32.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:32.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:32.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:32.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:32.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:32.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:32.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:32.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:36:32.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:36:32.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:32.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:36:32.702][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-04-15 20:36:32.703][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-04-15 20:36:32.704][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-04-15 20:36:32.908][biodb::testThat]
biodb.INFO [2024-04-15 20:36:32.909][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-04-15 20:36:32.911][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:36:32.911][biodb::testThat]
biodb.INFO [2024-04-15 20:36:32.954][biodb::testThat]
biodb.INFO [2024-04-15 20:36:32.955][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-04-15 20:36:32.956][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:36:32.957][biodb::testThat]
biodb.INFO [2024-04-15 20:36:32.964][biodb::testThat]
biodb.INFO [2024-04-15 20:36:32.965][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-04-15 20:36:32.966][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:36:32.967][biodb::testThat]
biodb.DEBUG[2024-04-15 20:36:32.970][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-04-15 20:36:32.973][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:32.974][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:32.976][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-04-15 20:36:37.110][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-04-15 20:36:48.157][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:36:48.159][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-04-15 20:36:48.174][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-04-15 20:36:49.082][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:36:49.083][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:36:49.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:49.085][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:36:49.086][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:36:49.087][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:36:49.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:36:49.089][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 20:36:49.091][biodb::testThat]
biodb.INFO [2024-04-15 20:36:49.092][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-04-15 20:36:49.093][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:36:49.094][biodb::testThat]
biodb.ERROR[2024-04-15 20:36:49.108][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-04-15 20:36:49.126][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-04-15 20:36:49.140][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 20:36:49.141][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-04-15 20:36:49.143][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-04-15 20:36:49.144][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 20:36:49.144][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.146][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.148][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-15 20:36:49.160][biodb::testContext]
biodb.INFO [2024-04-15 20:36:49.161][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 20:36:49.162][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-04-15 20:36:49.163][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 20:36:49.164][biodb::testContext]
biodb.INFO [2024-04-15 20:36:49.166][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 20:36:49.168][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 20:36:49.172][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 20:36:49.173][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 20:36:49.174][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 20:36:49.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.178][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 20:36:49.179][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 20:36:49.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.182][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 20:36:49.183][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 20:36:49.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.187][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 20:36:49.188][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 20:36:49.189][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 20:36:49.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.193][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 20:36:49.194][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 20:36:49.195][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 20:36:49.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.198][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 20:36:49.199][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 20:36:49.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.203][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 20:36:49.204][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 20:36:49.205][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 20:36:49.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.209][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 20:36:49.210][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 20:36:49.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.213][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 20:36:49.215][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 20:36:49.216][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 20:36:49.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.219][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 20:36:49.220][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 20:36:49.221][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 20:36:49.222][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 20:36:49.223][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 20:36:49.224][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 20:36:49.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.228][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 20:36:49.229][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 20:36:49.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.233][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 20:36:49.234][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 20:36:49.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.238][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 20:36:49.239][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 20:36:49.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.242][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 20:36:49.243][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 20:36:49.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.247][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 20:36:49.248][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 20:36:49.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.252][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 20:36:49.253][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 20:36:49.256][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 20:36:49.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.260][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 20:36:49.261][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 20:36:49.262][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 20:36:49.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.266][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 20:36:49.268][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.269][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 20:36:49.270][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.271][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:36:49.272][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.273][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.274][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.275][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.276][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 20:36:49.277][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:36:49.278][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.279][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 20:36:49.280][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:36:49.281][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.282][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.283][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 20:36:49.283][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 20:36:49.283][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 20:36:49.283][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 20:36:49.283][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 20:36:49.284][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:36:49.285][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:36:49.286][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:36:49.287][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:36:49.288][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:36:49.289][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:36:49.290][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.291][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.292][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:36:49.293][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:36:49.294][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.295][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.296][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 20:36:49.298][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.299][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 20:36:49.301][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.302][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:36:49.303][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.304][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.305][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.306][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.307][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 20:36:49.308][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:36:49.309][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.310][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 20:36:49.311][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:36:49.312][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.313][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.314][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 20:36:49.314][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 20:36:49.314][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 20:36:49.314][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 20:36:49.314][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 20:36:49.315][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:36:49.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:36:49.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:36:49.318][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:36:49.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:36:49.320][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:36:49.321][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.322][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.323][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:36:49.324][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:36:49.325][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.326][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.327][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 20:36:49.329][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.330][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 20:36:49.331][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.332][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:36:49.333][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.334][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.335][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.336][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.337][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 20:36:49.338][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:36:49.339][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.340][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 20:36:49.341][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:36:49.342][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.343][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.344][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.345][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:36:49.346][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:36:49.347][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:36:49.348][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:36:49.349][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:36:49.350][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:36:49.351][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.352][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.353][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:36:49.354][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:36:49.354][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.355][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.357][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 20:36:49.358][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.359][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 20:36:49.360][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.362][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:36:49.363][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.363][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.364][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.366][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.367][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 20:36:49.368][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:36:49.369][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.370][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 20:36:49.371][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:36:49.372][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.373][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.374][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.375][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:36:49.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:36:49.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:36:49.378][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:36:49.379][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:36:49.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:36:49.380][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.381][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.382][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:36:49.383][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:36:49.384][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.385][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.387][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 20:36:49.388][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.485][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 20:36:49.487][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 20:36:49.488][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 20:36:49.489][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 20:36:49.491][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 20:36:49.492][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 20:36:49.493][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 20:36:49.495][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 20:36:49.496][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 20:36:49.497][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 20:36:49.499][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 20:36:49.500][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 20:36:49.501][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 20:36:49.502][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 20:36:49.504][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 20:36:49.505][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 20:36:49.506][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 20:36:49.507][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 20:36:49.509][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 20:36:49.510][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 20:36:49.511][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 20:36:49.512][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 20:36:49.514][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 20:36:49.515][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 20:36:49.516][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 20:36:49.518][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 20:36:49.519][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 20:36:49.520][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 20:36:49.521][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 20:36:49.523][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 20:36:49.524][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 20:36:49.525][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 20:36:49.526][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 20:36:49.528][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 20:36:49.529][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 20:36:49.530][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 20:36:49.532][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 20:36:49.533][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 20:36:49.534][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 20:36:49.535][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 20:36:49.537][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 20:36:49.538][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 20:36:49.539][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 20:36:49.541][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 20:36:49.542][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 20:36:49.543][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 20:36:49.544][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 20:36:49.546][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 20:36:49.547][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 20:36:49.548][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 20:36:49.550][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 20:36:49.551][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 20:36:49.552][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 20:36:49.553][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 20:36:49.555][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 20:36:49.556][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 20:36:49.557][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 20:36:49.559][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 20:36:49.560][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 20:36:49.561][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 20:36:49.563][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 20:36:49.564][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 20:36:49.565][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 20:36:49.567][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 20:36:49.568][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 20:36:49.569][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 20:36:49.570][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 20:36:49.572][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 20:36:49.573][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 20:36:49.574][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 20:36:49.576][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 20:36:49.577][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 20:36:49.578][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 20:36:49.579][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 20:36:49.581][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 20:36:49.582][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 20:36:49.583][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 20:36:49.585][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 20:36:49.586][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 20:36:49.587][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 20:36:49.589][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 20:36:49.590][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 20:36:49.591][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 20:36:49.593][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 20:36:49.594][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 20:36:49.595][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 20:36:49.596][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.598][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.665][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[2024-04-15 20:36:49.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:36:49.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:36:49.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:36:49.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:36:49.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:36:49.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:36:49.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:36:49.751][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[2024-04-15 20:36:49.753][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-04-15 20:36:49.754][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 20:36:49.756][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.757][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.758][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.759][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:36:49.760][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.761][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.762][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.763][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.764][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 20:36:49.765][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:36:49.766][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.766][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-04-15 20:36:49.767][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:36:49.768][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-04-15 20:36:49.768][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-04-15 20:36:49.768][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-04-15 20:36:49.768][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-04-15 20:36:49.768][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-04-15 20:36:49.768][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-04-15 20:36:49.768][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-04-15 20:36:49.768][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-04-15 20:36:49.768][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-04-15 20:36:49.769][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 20:36:49.770][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 20:36:49.770][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 20:36:49.771][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:36:49.772][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:36:49.773][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:36:49.774][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:36:49.775][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:36:49.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:36:49.777][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:36:49.778][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 20:36:49.778][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-04-15 20:36:49.779][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:36:49.779][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:36:49.780][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 20:36:49.781][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:36:49.782][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-04-15 20:36:49.784][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 20:36:49.787][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 20:36:49.788][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-04-15 20:36:49.789][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 20:36:49.790][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-04-15 20:36:49.791][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 20:36:49.792][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 20:36:49.794][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-04-15 20:36:49.794][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-04-15 20:36:49.796][biodb::testThat]
biodb.INFO [2024-04-15 20:36:49.797][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-04-15 20:36:49.798][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:36:49.798][biodb::testThat]
biodb.DEBUG[2024-04-15 20:36:49.802][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-04-15 20:36:49.806][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:49.807][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:49.809][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-04-15 20:36:50.472][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-04-15 20:36:51.155][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:36:51.157][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-04-15 20:36:51.161][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-04-15 20:36:51.169][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-04-15 20:36:51.172][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:51.173][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:51.175][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-04-15 20:36:52.150][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-04-15 20:36:52.835][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:36:52.839][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-04-15 20:36:52.846][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-04-15 20:36:52.864][biodb::testThat]
biodb.INFO [2024-04-15 20:36:52.866][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-04-15 20:36:52.868][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:36:52.869][biodb::testThat]
biodb.INFO [2024-04-15 20:36:52.914][biodb::testThat]
biodb.INFO [2024-04-15 20:36:52.916][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-04-15 20:36:52.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:36:52.920][biodb::testThat]
biodb.DEBUG[2024-04-15 20:36:52.925][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-04-15 20:36:52.931][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:52.932][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:52.935][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-04-15 20:36:53.462][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-04-15 20:36:54.284][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:36:54.287][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-04-15 20:36:54.291][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-04-15 20:36:54.296][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-04-15 20:36:54.299][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 20:36:54.301][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-04-15 20:36:54.302][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 20:36:54.304][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-04-15 20:36:54.310][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-04-15 20:36:54.313][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:54.315][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:54.316][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-04-15 20:36:54.856][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-04-15 20:36:55.384][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:36:55.387][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-04-15 20:36:55.391][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-04-15 20:36:55.398][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-04-15 20:36:55.402][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:36:55.403][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:36:55.405][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-04-15 20:36:56.701][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-04-15 20:37:00.000][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:37:00.002][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-04-15 20:37:00.008][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-04-15 20:37:00.130][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-04-15 20:37:00.133][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 20:37:00.134][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 20:37:00.136][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-04-15 20:37:01.433][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-04-15 20:37:04.859][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 20:37:04.862][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-04-15 20:37:04.868][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-04-15 20:37:04.994][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 20:37:04.996][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-04-15 20:37:04.997][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-04-15 20:37:04.998][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 20:37:04.999][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.001][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.003][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-15 20:37:05.008][biodb::testContext]
biodb.INFO [2024-04-15 20:37:05.009][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 20:37:05.010][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-04-15 20:37:05.011][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 20:37:05.012][biodb::testContext]
biodb.INFO [2024-04-15 20:37:05.014][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 20:37:05.016][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 20:37:05.020][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 20:37:05.021][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 20:37:05.022][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 20:37:05.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.026][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 20:37:05.027][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 20:37:05.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.031][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 20:37:05.032][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 20:37:05.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.036][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 20:37:05.037][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 20:37:05.038][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 20:37:05.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.042][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 20:37:05.043][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 20:37:05.044][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 20:37:05.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.048][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 20:37:05.049][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 20:37:05.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.053][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 20:37:05.054][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 20:37:05.055][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 20:37:05.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.058][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[2024-04-15 20:37:05.059][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 20:37:05.060][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 20:37:05.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.064][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 20:37:05.065][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 20:37:05.066][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 20:37:05.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.070][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 20:37:05.071][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 20:37:05.072][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 20:37:05.073][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 20:37:05.074][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 20:37:05.075][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 20:37:05.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.079][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 20:37:05.080][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 20:37:05.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.128][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 20:37:05.129][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 20:37:05.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.133][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 20:37:05.134][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 20:37:05.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.138][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 20:37:05.139][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 20:37:05.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.143][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 20:37:05.144][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 20:37:05.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.148][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 20:37:05.149][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 20:37:05.152][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 20:37:05.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.156][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 20:37:05.157][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 20:37:05.158][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 20:37:05.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.162][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 20:37:05.163][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.164][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 20:37:05.165][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.166][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:37:05.167][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.168][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.169][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.170][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.171][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 20:37:05.172][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:37:05.173][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.174][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 20:37:05.175][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:37:05.176][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.177][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.178][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 20:37:05.178][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 20:37:05.178][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 20:37:05.178][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 20:37:05.178][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 20:37:05.179][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:37:05.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:37:05.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:37:05.182][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:37:05.183][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:37:05.184][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:37:05.185][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.186][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.187][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:37:05.188][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:37:05.189][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.190][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.191][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 20:37:05.193][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.194][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 20:37:05.195][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.196][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:37:05.197][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.198][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.199][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.200][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.201][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 20:37:05.202][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:37:05.203][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.204][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 20:37:05.205][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:37:05.206][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.207][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.208][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 20:37:05.208][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 20:37:05.208][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 20:37:05.208][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 20:37:05.208][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 20:37:05.209][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:37:05.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:37:05.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:37:05.212][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:37:05.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:37:05.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:37:05.215][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.216][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.217][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:37:05.218][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:37:05.218][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.219][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.221][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 20:37:05.222][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.223][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 20:37:05.224][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.225][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:37:05.226][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.227][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.228][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.229][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.230][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 20:37:05.231][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:37:05.232][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.233][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 20:37:05.234][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:37:05.235][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.236][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.237][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.238][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:37:05.239][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:37:05.240][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:37:05.241][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:37:05.242][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:37:05.243][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:37:05.244][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.245][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.246][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:37:05.247][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:37:05.248][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.249][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.250][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 20:37:05.252][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.253][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 20:37:05.254][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.255][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:37:05.256][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.257][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.258][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.259][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.260][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 20:37:05.261][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:37:05.262][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.263][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 20:37:05.264][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:37:05.265][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.266][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.267][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.268][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:37:05.269][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:37:05.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:37:05.271][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:37:05.272][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:37:05.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:37:05.273][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.274][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.275][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:37:05.276][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:37:05.277][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.278][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.280][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 20:37:05.281][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.317][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[2024-04-15 20:37:05.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.334][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[2024-04-15 20:37:05.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.351][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[2024-04-15 20:37:05.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.356][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 20:37:05.357][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 20:37:05.359][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 20:37:05.360][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 20:37:05.361][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 20:37:05.363][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 20:37:05.364][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 20:37:05.365][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 20:37:05.367][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 20:37:05.368][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 20:37:05.369][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 20:37:05.371][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 20:37:05.372][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 20:37:05.373][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 20:37:05.374][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 20:37:05.376][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 20:37:05.377][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 20:37:05.378][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 20:37:05.380][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 20:37:05.381][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 20:37:05.382][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 20:37:05.383][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 20:37:05.385][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 20:37:05.386][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 20:37:05.387][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 20:37:05.389][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 20:37:05.390][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 20:37:05.391][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 20:37:05.393][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 20:37:05.394][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 20:37:05.395][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 20:37:05.396][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 20:37:05.398][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 20:37:05.399][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 20:37:05.400][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 20:37:05.402][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 20:37:05.403][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 20:37:05.404][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 20:37:05.406][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 20:37:05.407][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 20:37:05.408][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 20:37:05.409][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 20:37:05.411][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 20:37:05.412][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 20:37:05.413][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 20:37:05.415][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 20:37:05.416][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 20:37:05.417][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 20:37:05.419][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 20:37:05.420][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 20:37:05.421][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 20:37:05.423][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 20:37:05.424][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 20:37:05.425][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 20:37:05.427][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 20:37:05.437][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 20:37:05.439][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 20:37:05.440][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 20:37:05.442][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 20:37:05.443][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 20:37:05.444][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 20:37:05.446][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 20:37:05.447][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 20:37:05.448][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 20:37:05.450][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 20:37:05.451][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 20:37:05.452][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 20:37:05.453][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 20:37:05.455][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 20:37:05.456][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 20:37:05.457][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 20:37:05.459][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 20:37:05.460][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 20:37:05.461][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 20:37:05.463][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 20:37:05.464][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 20:37:05.465][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 20:37:05.466][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 20:37:05.468][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 20:37:05.469][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 20:37:05.470][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 20:37:05.472][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 20:37:05.473][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 20:37:05.474][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 20:37:05.476][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 20:37:05.477][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 20:37:05.478][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.479][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 20:37:05.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:05.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:05.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:05.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:05.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:05.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 20:37:05.579][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-04-15 20:37:05.581][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 20:37:05.582][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.583][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.584][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.585][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 20:37:05.586][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.587][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.588][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.589][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.590][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 20:37:05.591][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 20:37:05.592][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.593][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-04-15 20:37:05.594][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 20:37:05.594][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-04-15 20:37:05.594][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-04-15 20:37:05.594][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-04-15 20:37:05.594][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-04-15 20:37:05.594][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-04-15 20:37:05.594][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-04-15 20:37:05.594][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-04-15 20:37:05.594][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-04-15 20:37:05.594][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-04-15 20:37:05.595][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 20:37:05.596][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 20:37:05.596][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 20:37:05.597][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 20:37:05.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:37:05.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:37:05.600][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 20:37:05.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 20:37:05.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 20:37:05.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 20:37:05.604][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 20:37:05.604][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-04-15 20:37:05.604][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 20:37:05.605][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 20:37:05.606][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 20:37:05.607][self$setPropertyValue]
biodb.DEBUG[2024-04-15 20:37:05.608][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-04-15 20:37:05.610][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 20:37:05.613][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 20:37:05.614][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-04-15 20:37:05.615][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 20:37:05.616][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-04-15 20:37:05.617][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 20:37:05.618][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 20:37:05.619][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-04-15 20:37:05.620][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-04-15 20:37:05.622][biodb::testThat]
biodb.INFO [2024-04-15 20:37:05.623][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-04-15 20:37:05.623][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 20:37:05.624][biodb::testThat]
biodb.DEBUG[2024-04-15 20:37:05.628][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-04-15 20:37:05.631][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 20:37:05.633][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-04-15 20:37:05.634][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 20:37:05.679][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-04-15 20:37:06.506][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-04-15 20:37:06.507][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-04-15 20:37:06.509][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-04-15 20:37:06.510][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-04-15 20:37:06.512][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-04-15 20:37:06.513][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 20:37:06.514][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-04-15 20:37:06.515][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 20:37:06.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:37:06.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:06.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:06.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:06.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:06.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:06.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:37:06.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.545][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 20:37:06.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 20:37:06.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.549][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 20:37:06.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 20:37:06.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.553][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.556][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.560][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.568][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 20:37:06.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.572][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 20:37:06.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.575][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:06.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:06.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.579][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:06.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:06.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.591][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 20:37:06.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.595][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-15 20:37:06.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.606][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 20:37:06.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.610][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.628][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.632][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.640][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:37:06.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:37:06.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:06.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:06.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:06.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:06.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:06.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:37:06.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.685][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 20:37:06.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 20:37:06.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.689][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 20:37:06.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 20:37:06.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.693][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.697][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.701][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.705][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.709][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 20:37:06.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.713][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 20:37:06.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.717][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:06.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:06.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.721][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:06.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:06.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.733][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 20:37:06.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.736][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-15 20:37:06.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.744][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.748][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 20:37:06.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.752][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.755][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.763][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 20:37:06.815][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-04-15 20:37:06.817][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-15 20:37:06.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:37:06.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:06.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:06.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:06.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:06.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:06.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:37:06.829][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 20:37:06.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 20:37:06.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.833][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 20:37:06.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 20:37:06.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.836][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-15 20:37:06.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-15 20:37:06.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.840][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-15 20:37:06.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-15 20:37:06.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.844][private$selectFields] Fields none
biodb.TRACE[2024-04-15 20:37:06.844][private$selectFields]
biodb.TRACE[2024-04-15 20:37:06.845][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-04-15 20:37:06.846][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 20:37:06.847][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:37:06.848][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.849][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.851][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.852][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.853][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.854][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.855][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.856][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.858][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.859][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.860][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.862][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.862][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.863][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.865][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.866][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:06.867][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:06.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.869][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.870][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.871][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.872][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.873][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.874][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.876][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.877][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.878][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.880][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.881][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.882][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.883][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.884][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.885][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.887][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.888][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.889][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.891][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.892][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.893][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.894][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.895][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:06.896][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:06.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.898][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.899][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.900][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.901][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.902][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.903][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.905][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.906][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:37:06.907][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:37:06.908][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.909][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.911][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.911][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.912][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.914][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.915][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.916][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.918][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.919][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.920][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.921][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.922][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.923][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.925][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.926][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:06.927][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:06.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.928][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.929][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:06.930][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:06.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.932][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.933][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.934][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:06.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.936][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.937][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-04-15 20:37:06.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:06.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:06.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:06.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.960][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.964][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.968][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:06.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.972][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.975][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.979][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:06.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:06.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.994][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:06.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:06.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:06.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:06.998][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:06.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:07.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.002][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:07.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:07.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.006][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:07.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:07.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:07.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:07.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:07.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:07.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.017][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.020][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.024][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.034][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-04-15 20:37:07.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 20:37:07.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:07.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:07.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:07.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:07.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:07.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 20:37:07.045][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 20:37:07.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 20:37:07.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.049][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 20:37:07.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 20:37:07.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.053][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-15 20:37:07.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-15 20:37:07.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.056][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-15 20:37:07.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-15 20:37:07.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.060][private$selectFields] Fields none
biodb.TRACE[2024-04-15 20:37:07.061][private$selectFields]
biodb.TRACE[2024-04-15 20:37:07.062][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-04-15 20:37:07.063][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 20:37:07.064][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:37:07.065][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:07.066][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:07.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.067][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.068][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:07.069][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:07.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.071][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.072][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:07.073][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:07.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.075][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.076][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:07.077][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:07.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.078][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.079][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:07.080][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:07.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.082][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.083][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:07.084][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:07.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.086][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.087][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:07.088][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:07.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.089][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.101][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.103][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.105][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.105][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:07.107][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:07.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.108][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.109][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:07.110][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:07.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.112][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.113][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:07.114][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:07.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.116][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.117][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:07.118][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:07.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.119][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.120][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:07.121][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:07.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.123][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.124][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:07.125][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:07.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.127][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.127][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:07.128][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:07.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.130][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.131][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.132][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.134][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.135][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:37:07.136][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-04-15 20:37:07.137][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:07.138][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:07.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.139][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.140][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:07.141][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:07.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.143][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.144][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:07.145][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:07.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.147][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.148][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:07.149][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:07.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.151][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.152][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:07.152][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:07.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.154][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.155][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:07.156][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:07.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.158][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.159][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:07.160][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:07.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.161][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.162][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.163][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.165][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.166][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-04-15 20:37:07.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:07.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:07.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:07.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:07.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 20:37:07.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 20:37:07.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:07.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:07.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:07.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:07.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 20:37:07.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 20:37:07.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.190][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:07.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:07.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.194][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:07.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:07.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.197][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:07.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 20:37:07.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.201][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:07.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:07.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.205][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:07.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:07.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.209][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:07.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 20:37:07.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:07.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:07.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:07.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:07.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:07.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 20:37:07.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.224][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:07.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:07.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.227][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:07.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:07.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.231][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 20:37:07.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 20:37:07.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:07.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:07.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:07.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:07.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 20:37:07.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 20:37:07.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.246][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.250][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.254][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 20:37:07.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 20:37:07.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 20:37:07.261][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-04-15 20:37:07.262][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-04-15 20:37:07.263][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-04-15 20:37:07.268][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 20:37:07.270][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-04-15 20:37:07.271][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-04-15 20:37:07.271][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 20:37:07.272][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 20:37:07.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 20:37:07.274][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 20:37:07.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 20:37:07.276][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 20:37:07.276][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".
[ 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
LipidmapsStructureConn1.4580.0563.267
LipidmapsStructureEntry0.2430.0030.248