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This page was generated on 2024-07-09 17:41 -0400 (Tue, 09 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4709
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-07-07 14:00 -0400 (Sun, 07 Jul 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for biodbLipidmaps on merida1

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

raw results


Summary

Package: biodbLipidmaps
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-07-08 01:10:11 -0400 (Mon, 08 Jul 2024)
EndedAt: 2024-07-08 01:15:55 -0400 (Mon, 08 Jul 2024)
EllapsedTime: 344.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
LipidmapsStructureConn 4.39  1.246  11.548
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck/00check.log’
for details.

Installation output

biodbLipidmaps.Rcheck/00install.out

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


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

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


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

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-07-08 01:13:03.997][biodb::testContext]
biodb.INFO [2024-07-08 01:13:04.006][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 01:13:04.009][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-07-08 01:13:04.012][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 01:13:04.014][biodb::testContext]
biodb.INFO [2024-07-08 01:13:04.061][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-08 01:13:04.066][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-08 01:13:04.110][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 01:13:04.124][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-08 01:13:04.128][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-08 01:13:04.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.143][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-08 01:13:04.310][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-08 01:13:04.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.372][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-08 01:13:04.375][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-08 01:13:04.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.395][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-08 01:13:04.398][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-08 01:13:04.400][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-08 01:13:04.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.419][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-08 01:13:04.421][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-08 01:13:04.437][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-08 01:13:04.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.445][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-08 01:13:04.460][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-08 01:13:04.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.479][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-08 01:13:04.483][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-08 01:13:04.485][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-08 01:13:04.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.506][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-08 01:13:04.509][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-08 01:13:04.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.528][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-08 01:13:04.530][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-08 01:13:04.533][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-08 01:13:04.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.572][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-08 01:13:04.575][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-08 01:13:04.578][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-08 01:13:04.580][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-08 01:13:04.583][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-08 01:13:04.585][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-08 01:13:04.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.604][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[2024-07-08 01:13:04.607][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-08 01:13:04.609][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-08 01:13:04.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.633][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-08 01:13:04.647][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-08 01:13:04.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.656][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-08 01:13:04.668][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-08 01:13:04.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.688][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-08 01:13:04.702][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-08 01:13:04.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.766][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-08 01:13:04.769][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-08 01:13:04.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.778][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-08 01:13:04.781][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-08 01:13:04.803][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-08 01:13:04.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.812][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-08 01:13:04.815][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-08 01:13:04.823][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-08 01:13:04.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:04.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:04.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:04.843][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-08 01:13:05.039][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:05.138][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-08 01:13:05.141][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.155][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:13:05.158][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.160][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:13:05.163][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:05.172][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:13:05.174][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 01:13:05.177][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:13:05.179][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.186][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-08 01:13:05.195][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:13:05.198][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.203][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.206][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 01:13:05.206][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 01:13:05.206][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 01:13:05.206][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 01:13:05.206][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 01:13:05.221][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:13:05.224][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:13:05.226][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:13:05.228][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:13:05.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:13:05.243][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:13:05.245][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:13:05.248][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.265][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:13:05.267][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:13:05.270][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:05.273][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.288][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-08 01:13:05.293][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:05.302][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 01:13:05.304][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.307][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:13:05.309][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.329][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:13:05.333][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:05.338][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:13:05.341][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 01:13:05.354][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:13:05.369][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.394][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-08 01:13:05.398][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:13:05.401][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.414][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.417][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 01:13:05.417][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 01:13:05.417][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 01:13:05.417][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 01:13:05.417][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 01:13:05.419][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:13:05.421][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:13:05.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:13:05.438][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:13:05.440][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:13:05.442][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:13:05.444][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:13:05.446][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.448][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:13:05.450][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:13:05.452][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:05.463][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.466][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-08 01:13:05.470][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.486][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-08 01:13:05.488][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.492][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:13:05.494][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.510][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:13:05.512][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:05.515][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:13:05.517][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 01:13:05.531][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:13:05.534][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:05.536][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-08 01:13:05.538][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:13:05.553][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.556][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.559][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.561][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:13:05.590][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:13:05.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:13:05.594][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:13:05.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:13:05.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:13:05.609][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:13:05.613][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.615][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:13:05.617][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:13:05.625][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:05.628][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.630][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-08 01:13:05.641][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.643][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 01:13:05.646][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.648][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:13:05.670][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.673][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:13:05.685][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:05.687][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:13:05.690][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 01:13:05.692][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:13:05.694][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:05.707][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-08 01:13:05.710][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:13:05.713][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.715][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:05.725][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.727][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:13:05.729][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:13:05.732][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:13:05.740][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:13:05.742][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:13:05.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:13:05.746][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:13:05.749][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.763][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:13:05.765][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:13:05.768][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:05.770][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:05.791][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 01:13:05.793][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:05.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:05.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:05.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:05.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:05.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:05.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:05.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:05.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:05.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:05.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:05.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:05.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:05.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:05.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:05.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:05.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:05.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:05.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:05.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:05.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:05.906][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[2024-07-08 01:13:05.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:05.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:05.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:05.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:05.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:05.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:05.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:05.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:05.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:05.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:05.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:05.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:05.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:05.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:05.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:05.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:05.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:05.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:05.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:05.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:05.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:05.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:06.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:06.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:06.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:06.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:06.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:06.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:06.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:06.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:06.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:06.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:06.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:06.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:06.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:06.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:06.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:06.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:06.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:06.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:06.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:06.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:06.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:06.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:06.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:06.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:06.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:06.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:06.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:06.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:06.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:06.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:06.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:06.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:06.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:06.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:06.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:06.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:06.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:06.197][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[2024-07-08 01:13:06.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:06.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:06.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:06.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:06.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:06.224][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-08 01:13:06.246][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-08 01:13:06.249][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-08 01:13:06.265][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-08 01:13:06.269][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-08 01:13:06.275][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-08 01:13:06.291][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-08 01:13:06.308][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-08 01:13:06.311][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-08 01:13:06.315][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-08 01:13:06.328][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-08 01:13:06.332][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-08 01:13:06.359][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-08 01:13:06.362][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-08 01:13:06.366][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-08 01:13:06.384][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-08 01:13:06.388][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-08 01:13:06.402][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-08 01:13:06.424][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-08 01:13:06.428][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-08 01:13:06.432][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-08 01:13:06.446][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-08 01:13:06.450][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-08 01:13:06.470][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-08 01:13:06.473][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-08 01:13:06.479][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-08 01:13:06.492][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-08 01:13:06.507][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-08 01:13:06.510][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-08 01:13:06.514][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-08 01:13:06.529][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-08 01:13:06.533][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-08 01:13:06.559][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-08 01:13:06.563][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-08 01:13:06.567][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-08 01:13:06.580][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-08 01:13:06.583][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-08 01:13:06.598][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-08 01:13:06.602][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-08 01:13:06.605][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-08 01:13:06.621][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-08 01:13:06.625][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-08 01:13:06.630][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-08 01:13:06.648][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-08 01:13:06.664][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-08 01:13:06.667][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-08 01:13:06.687][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-08 01:13:06.693][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-08 01:13:06.707][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-08 01:13:06.712][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-08 01:13:06.717][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-08 01:13:06.728][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-08 01:13:06.731][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-08 01:13:06.734][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-08 01:13:06.749][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-08 01:13:06.753][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-08 01:13:06.757][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-08 01:13:06.777][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-08 01:13:06.794][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-08 01:13:06.797][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-08 01:13:06.801][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-08 01:13:06.815][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-08 01:13:06.818][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-08 01:13:06.821][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-08 01:13:06.838][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-08 01:13:06.842][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-08 01:13:06.845][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-08 01:13:06.865][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-08 01:13:06.870][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-08 01:13:06.887][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-08 01:13:06.890][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-08 01:13:06.894][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-08 01:13:06.910][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-08 01:13:06.917][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-08 01:13:06.920][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-08 01:13:06.937][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-08 01:13:06.942][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-08 01:13:06.955][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-08 01:13:06.959][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-08 01:13:06.965][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-08 01:13:06.979][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-08 01:13:06.983][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-08 01:13:06.987][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-08 01:13:07.025][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-08 01:13:07.029][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-08 01:13:07.049][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 01:13:07.051][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.069][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.355][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[2024-07-08 01:13:07.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.492][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[2024-07-08 01:13:07.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.636][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[2024-07-08 01:13:07.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.677][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[2024-07-08 01:13:07.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:13:07.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:07.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:07.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:07.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:07.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:07.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:07.828][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-07-08 01:13:07.901][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-07-08 01:13:07.906][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:07.909][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-08 01:13:07.925][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:07.927][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:13:07.930][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:07.944][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:13:07.947][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:07.949][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:13:07.952][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 01:13:07.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:13:07.970][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:07.972][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-07-08 01:13:07.975][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:13:07.988][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-07-08 01:13:07.988][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-07-08 01:13:07.988][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-07-08 01:13:07.988][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-07-08 01:13:07.988][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-07-08 01:13:07.988][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-07-08 01:13:07.988][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-07-08 01:13:07.988][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-07-08 01:13:07.988][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-07-08 01:13:08.004][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-08 01:13:08.006][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 01:13:08.006][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 01:13:08.009][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:13:08.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:13:08.025][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:13:08.028][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:13:08.031][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:13:08.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:13:08.035][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:13:08.052][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-08 01:13:08.052][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-07-08 01:13:08.055][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:13:08.057][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:13:08.059][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-08 01:13:08.071][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:13:08.097][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-07-08 01:13:08.111][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-08 01:13:08.204][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-07-08 01:13:08.220][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-07-08 01:13:08.238][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-07-08 01:13:08.254][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-07-08 01:13:08.262][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-08 01:13:08.282][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-08 01:13:08.287][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-07-08 01:13:08.290][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-07-08 01:13:08.327][biodb::testThat]
biodb.INFO [2024-07-08 01:13:08.330][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-07-08 01:13:08.351][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:08.354][biodb::testThat]
biodb.TRACE[2024-07-08 01:13:08.461][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-07-08 01:13:08.467][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-07-08 01:13:08.485][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-08 01:13:08.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:08.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:08.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:08.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:08.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:08.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:08.571][FUN] Functions in observer BiodbConfig: [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[2024-07-08 01:13:08.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:08.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:08.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:08.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:08.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:08.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:08.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:08.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:08.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 01:13:08.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 01:13:08.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:08.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:08.846][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-08 01:13:08.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-08 01:13:08.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:08.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:08.868][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 01:13:08.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 01:13:08.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:08.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:08.884][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:08.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:08.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:08.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.085][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:09.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:09.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.129][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:09.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:09.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.160][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:09.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:09.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.187][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-08 01:13:09.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:09.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.223][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-08 01:13:09.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:09.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.251][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:09.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:09.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.299][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:09.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:09.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:09.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:09.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.366][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:09.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:09.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.403][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-08 01:13:09.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:09.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.432][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-08 01:13:09.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:09.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:09.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:09.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:09.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:09.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.486][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-08 01:13:09.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:09.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:09.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:09.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:09.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:09.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:09.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:09.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:09.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:09.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:09.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:10.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:10.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:10.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.040][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.061][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.104][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:13:10.259][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-07-08 01:13:10.265][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-08 01:13:10.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-08 01:13:10.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.276][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-08 01:13:10.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-08 01:13:10.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.286][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-08 01:13:10.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-08 01:13:10.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.295][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-08 01:13:10.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-08 01:13:10.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.485][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.729][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.789][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.798][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:10.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.905][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.908][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.913][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:10.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:10.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:10.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:10.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:11.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:11.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.057][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:11.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:11.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:11.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:11.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.100][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:11.102][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:11.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.130][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:11.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:11.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.272][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:11.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:11.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.285][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:11.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:11.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.296][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:11.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:11.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.305][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:11.319][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:11.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.326][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.329][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:11.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:11.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.507][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:11.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:11.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.538][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:11.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:11.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:11.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:11.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.602][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:11.606][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:11.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.610][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.613][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:11.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:11.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:11.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:11.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:11.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:11.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:11.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:11.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.770][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:11.773][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:11.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.777][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:11.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:11.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.820][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:11.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:11.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.839][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:11.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:11.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.852][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:11.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:11.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.907][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:11.909][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:11.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.911][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.913][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:11.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:11.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.955][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:11.963][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:11.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.968][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:11.979][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:11.980][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:11.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:11.993][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.015][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:12.018][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:12.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.022][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.032][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:12.035][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:12.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.040][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.053][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:12.056][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.085][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.103][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:12.106][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:12.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.113][ef$get] fields variable is a list.
biodb.INFO [2024-07-08 01:13:12.146][biodb::testThat]
biodb.INFO [2024-07-08 01:13:12.147][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-08 01:13:12.148][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:12.150][biodb::testThat]
biodb.DEBUG[2024-07-08 01:13:12.192][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-07-08 01:13:12.208][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 01:13:12.220][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-07-08 01:13:12.223][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 01:13:12.228][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-07-08 01:13:12.229][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 01:13:12.286][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-07-08 01:13:12.287][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-08 01:13:12.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:12.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:12.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:12.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:12.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:12.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:12.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:13:12.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:12.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:12.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:12.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:12.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 01:13:12.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 01:13:12.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 01:13:12.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 01:13:12.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.376][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-08 01:13:12.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-08 01:13:12.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.388][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 01:13:12.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 01:13:12.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.399][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:12.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:12.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.405][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:12.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:12.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.412][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:12.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:12.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.424][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:12.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:12.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.433][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-08 01:13:12.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:12.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.439][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-08 01:13:12.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:12.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.465][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:12.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:12.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:12.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:12.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:12.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:12.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.522][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-08 01:13:12.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.533][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-08 01:13:12.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:12.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.570][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:12.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.576][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-08 01:13:12.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:12.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:12.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.618][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:12.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:12.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:12.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:12.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.643][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:12.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:12.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.648][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:12.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:12.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:12.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:12.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.686][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:12.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:12.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:12.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:12.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:12.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:12.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:12.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:12.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:12.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:12.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:12.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:12.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:12.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:12.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:13:12.855][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-07-08 01:13:12.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-08 01:13:12.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-08 01:13:12.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-08 01:13:12.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-08 01:13:12.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:12.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-08 01:13:12.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-08 01:13:12.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:12.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-08 01:13:13.006][biodb::testThat]
biodb.INFO [2024-07-08 01:13:13.008][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-08 01:13:13.011][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:13.014][biodb::testThat]
biodb.TRACE[2024-07-08 01:13:13.031][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:13.033][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:13.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:13.051][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:13:13.055][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-07-08 01:13:13.200][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:13.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:13.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:13.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:13.223][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:13.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:13.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:13.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:13.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:13.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:13.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:13.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:13:13.279][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-07-08 01:13:13.301][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[2024-07-08 01:13:13.422][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 01:13:13.534][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-07-08 01:13:13.537][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 01:13:13.549][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-07-08 01:13:13.555][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-07-08 01:13:13.617][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:13.619][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:13.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:13.624][ef$get] fields variable is a list.
biodb.INFO [2024-07-08 01:13:13.646][biodb::testThat]
biodb.INFO [2024-07-08 01:13:13.660][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-07-08 01:13:13.662][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:13.665][biodb::testThat]
biodb.TRACE[2024-07-08 01:13:13.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:13.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:13.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:13.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:13.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:13.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:13.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:13.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:13.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:13.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:13.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:13:14.518][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[2024-07-08 01:13:14.535][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 01:13:14.539][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-07-08 01:13:14.556][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 01:13:14.560][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-07-08 01:13:14.656][biodb::testThat]
biodb.INFO [2024-07-08 01:13:14.659][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-07-08 01:13:14.661][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:14.664][biodb::testThat]
biodb.TRACE[2024-07-08 01:13:14.799][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-08 01:13:14.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-08 01:13:14.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:14.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:14.833][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-08 01:13:14.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-08 01:13:14.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:14.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:14.856][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-08 01:13:14.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-08 01:13:14.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:14.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:14.883][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-08 01:13:14.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-08 01:13:14.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:14.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:15.239][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-08 01:13:15.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-08 01:13:15.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:15.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:15.264][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-08 01:13:15.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-08 01:13:15.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:15.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:15.309][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-08 01:13:15.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-08 01:13:15.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:15.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:15.338][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-08 01:13:15.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-08 01:13:15.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:15.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-08 01:13:15.392][biodb::testThat]
biodb.INFO [2024-07-08 01:13:15.395][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-08 01:13:15.398][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:15.412][biodb::testThat]
biodb.INFO [2024-07-08 01:13:15.448][biodb::testThat]
biodb.INFO [2024-07-08 01:13:15.458][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-08 01:13:15.462][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:15.466][biodb::testThat]
biodb.INFO [2024-07-08 01:13:15.508][biodb::testThat]
biodb.INFO [2024-07-08 01:13:15.525][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-08 01:13:15.530][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:15.534][biodb::testThat]
biodb.DEBUG[2024-07-08 01:13:15.568][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-07-08 01:13:17.129][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-07-08 01:13:17.542][biodb::testThat]
biodb.INFO [2024-07-08 01:13:17.545][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-08 01:13:17.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:17.549][biodb::testThat]
biodb.TRACE[2024-07-08 01:13:17.562][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:17.565][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:17.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:17.569][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:17.571][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:17.573][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:17.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:17.577][ef$get] fields variable is a list.
biodb.INFO [2024-07-08 01:13:17.581][biodb::testThat]
biodb.INFO [2024-07-08 01:13:17.583][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-07-08 01:13:17.586][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:17.588][biodb::testThat]
biodb.TRACE[2024-07-08 01:13:17.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:17.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:17.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:17.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:17.623][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:17.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:17.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:17.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:17.632][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:17.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:17.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:17.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:13:18.009][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[2024-07-08 01:13:18.016][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 01:13:18.018][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-07-08 01:13:18.025][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 01:13:18.029][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-07-08 01:13:18.177][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[2024-07-08 01:13:18.182][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 01:13:18.184][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-07-08 01:13:18.185][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 01:13:18.187][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-07-08 01:13:18.230][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-08 01:13:18.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-08 01:13:18.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:18.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:18.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 01:13:18.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 01:13:18.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:18.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:18.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:18.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:18.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:18.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:18.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:18.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:18.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:18.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:18.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:18.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:18.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:18.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:18.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:18.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:18.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:18.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:18.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:18.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:18.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:18.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:13:18.323][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[2024-07-08 01:13:18.335][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 01:13:18.338][cch$loadFileContent] Trying to load 1 files from cache: [1]: "304383a7dc8c451be84009e31d831359".
biodb.TRACE[2024-07-08 01:13:18.341][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 01:13:18.582][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content".
biodb.DEBUG[2024-07-08 01:13:23.278][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[2024-07-08 01:13:23.286][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 01:13:23.290][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7f71825f1888a7b29e4b8407502d21e3".
biodb.TRACE[2024-07-08 01:13:23.304][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 01:13:23.307][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content".
biodb.DEBUG[2024-07-08 01:13:23.385][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[2024-07-08 01:13:23.392][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 01:13:23.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "fd41c675dd237f33cdaafcbb15058c54".
biodb.TRACE[2024-07-08 01:13:23.409][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 01:13:23.439][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content".
biodb.TRACE[2024-07-08 01:13:23.473][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-08 01:13:23.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-08 01:13:23.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:23.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-08 01:13:23.506][biodb::testThat]
biodb.INFO [2024-07-08 01:13:23.519][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-07-08 01:13:23.523][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:23.551][biodb::testThat]
biodb.TRACE[2024-07-08 01:13:23.557][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-08 01:13:23.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-08 01:13:23.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:23.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:23.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 01:13:23.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 01:13:23.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:23.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:23.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:23.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:23.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:23.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:23.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:23.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:23.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:23.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:23.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:23.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:23.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:23.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:23.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:23.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:23.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:23.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:13:23.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:23.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:23.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:23.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:23.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:23.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:23.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:23.735][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[2024-07-08 01:13:23.802][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 01:13:23.804][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-07-08 01:13:23.806][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 01:13:23.851][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-07-08 01:13:27.354][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-07-08 01:13:27.618][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-08 01:13:27.644][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-07-08 01:13:27.649][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-07-08 01:13:27.660][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv".
biodb.DEBUG[2024-07-08 01:13:27.663][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 01:13:27.666][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-07-08 01:13:27.681][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-08 01:13:27.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:27.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:27.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:27.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:27.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:27.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:27.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:13:27.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:27.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:27.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:27.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:27.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:27.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:27.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:27.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:27.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 01:13:27.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 01:13:27.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:27.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:27.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 01:13:27.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 01:13:27.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:27.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:27.883][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-08 01:13:27.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-08 01:13:27.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:27.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:27.902][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 01:13:27.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 01:13:27.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:27.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:27.923][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:27.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:27.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:27.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:27.933][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:27.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:27.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:27.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:27.949][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:27.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:27.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:27.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:27.972][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:27.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:27.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:27.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:27.991][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-08 01:13:27.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:27.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.067][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-08 01:13:28.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:28.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.090][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:28.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:28.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.132][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:28.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:28.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:28.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:28.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.185][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:28.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:28.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.207][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-08 01:13:28.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:28.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.272][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-08 01:13:28.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:28.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:28.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:28.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:28.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:28.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.452][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-08 01:13:28.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:28.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.525][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:28.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:28.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.533][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:28.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:28.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:28.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:28.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.630][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:28.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:28.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:28.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:28.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:28.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:28.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:28.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:28.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:13:28.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:28.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:28.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:28.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:28.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:28.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:28.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:13:28.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:28.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:28.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:28.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:28.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:28.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:28.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 01:13:29.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 01:13:29.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.026][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-08 01:13:29.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-08 01:13:29.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.042][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 01:13:29.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 01:13:29.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.083][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:29.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:29.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.115][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:29.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-08 01:13:29.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.131][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:29.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:29.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.162][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:29.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-08 01:13:29.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.185][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-08 01:13:29.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:29.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.218][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-08 01:13:29.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:29.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.251][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:29.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:29.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 01:13:29.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 01:13:29.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:29.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:29.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.318][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:29.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:29.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.344][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-08 01:13:29.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:29.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.376][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-08 01:13:29.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:29.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:29.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:29.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:13:29.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:29.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.456][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-08 01:13:29.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:13:29.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.479][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:29.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:29.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.519][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:29.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:29.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:29.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:29.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.568][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:29.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:29.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:29.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:29.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:29.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:29.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:29.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:29.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:29.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:29.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:29.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:29.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:29.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:29.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:29.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:29.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:29.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:29.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:13:29.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:13:29.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:13:29.849][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-07-08 01:13:29.906][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-08 01:13:29.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:29.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:29.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:29.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:29.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:29.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:29.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:13:29.971][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:29.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:29.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:29.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:29.990][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:29.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.009][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:30.012][private$selectFields]
biodb.TRACE[2024-07-08 01:13:30.029][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 01:13:30.031][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 01:13:30.033][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:30.039][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.051][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.056][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.059][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.073][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.078][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.081][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:30.097][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:30.101][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.104][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.121][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.124][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-08 01:13:30.126][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.149][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.169][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.240][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-07-08 01:13:30.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:30.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:30.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:30.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:30.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:30.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:30.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:13:30.296][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.305][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.350][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:30.352][private$selectFields]
biodb.TRACE[2024-07-08 01:13:30.367][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 01:13:30.370][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 01:13:30.372][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:30.375][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.387][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.392][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.406][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.409][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.413][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.427][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:30.430][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:30.433][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.437][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.454][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.456][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-08 01:13:30.459][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.493][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.514][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.539][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-07-08 01:13:30.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:30.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:30.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:30.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:30.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:30.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:30.581][FUN] Functions in observer BiodbConfig: [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[2024-07-08 01:13:30.599][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.621][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.643][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:30.645][private$selectFields]
biodb.TRACE[2024-07-08 01:13:30.648][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 01:13:30.650][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 01:13:30.659][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:30.662][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.664][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.677][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.680][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.683][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.701][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.703][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:30.706][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:30.708][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.722][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.729][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.743][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-08 01:13:30.746][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.770][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.786][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:30.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.806][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-07-08 01:13:30.808][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-08 01:13:30.820][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-08 01:13:30.861][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-08 01:13:30.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-08 01:13:30.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-08 01:13:30.904][biodb::testThat]
biodb.INFO [2024-07-08 01:13:30.908][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-07-08 01:13:30.911][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:30.913][biodb::testThat]
biodb.TRACE[2024-07-08 01:13:30.921][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-08 01:13:30.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-08 01:13:30.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 01:13:30.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 01:13:30.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:30.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:30.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:30.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:30.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:30.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:31.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:31.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:31.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:31.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:31.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:31.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:31.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:31.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:31.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:31.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:13:31.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:31.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:31.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:31.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:31.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:31.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:31.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:31.513][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-07-08 01:13:31.529][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 01:13:31.548][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5652f5994fce967a05a065a71bac3ed6".
biodb.TRACE[2024-07-08 01:13:31.551][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 01:13:31.651][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content".
biodb.DEBUG[2024-07-08 01:13:34.527][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-08 01:13:34.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:34.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:34.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:34.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:34.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:34.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:34.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:13:34.712][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:34.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:34.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:34.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:34.723][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:34.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:34.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:34.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:34.888][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:34.891][private$selectFields]
biodb.TRACE[2024-07-08 01:13:34.908][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 01:13:34.912][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 01:13:34.915][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:34.917][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:34.930][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:34.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:34.938][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:34.941][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:34.944][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:34.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:34.948][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:34.951][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:35.008][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:35.025][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.028][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.033][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.047][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-08 01:13:35.050][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.074][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.089][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.116][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-07-08 01:13:35.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:35.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:35.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:35.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:35.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:35.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:35.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:13:35.177][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.196][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.217][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:35.219][private$selectFields]
biodb.TRACE[2024-07-08 01:13:35.232][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 01:13:35.234][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 01:13:35.237][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:35.239][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.250][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.255][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.258][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.273][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.279][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.290][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:35.293][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:35.296][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.299][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.313][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.315][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-08 01:13:35.319][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.351][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.371][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.387][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-07-08 01:13:35.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:35.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:35.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:35.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:35.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:35.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:35.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:13:35.433][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.459][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.486][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:35.504][private$selectFields]
biodb.TRACE[2024-07-08 01:13:35.507][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 01:13:35.509][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 01:13:35.512][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:35.526][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.529][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.533][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.550][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.553][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.565][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.567][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:35.570][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:35.572][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.574][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.596][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.598][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-08 01:13:35.613][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.641][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.666][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:35.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.688][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-07-08 01:13:35.690][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-08 01:13:35.693][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-08 01:13:35.732][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-08 01:13:35.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-08 01:13:35.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-08 01:13:35.783][biodb::testThat]
biodb.INFO [2024-07-08 01:13:35.786][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-07-08 01:13:35.789][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:35.801][biodb::testThat]
biodb.TRACE[2024-07-08 01:13:35.807][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-08 01:13:35.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-08 01:13:35.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 01:13:35.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 01:13:35.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:35.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:35.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.877][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:35.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:35.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:35.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:35.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:35.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:35.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:13:35.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:35.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:13:36.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:36.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:36.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:36.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:36.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:36.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:36.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:36.084][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.INFO [2024-07-08 01:13:36.112][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.DEBUG[2024-07-08 01:13:36.115][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:13:36.118][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:13:36.123][private$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[2024-07-08 01:13:40.098][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[2024-07-08 01:13:48.446][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 01:13:48.469][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-07-08 01:13:48.833][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-07-08 01:13:52.683][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-08 01:13:52.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:52.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:52.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:52.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:52.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:52.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:52.735][FUN] Functions in observer BiodbConfig: [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[2024-07-08 01:13:52.738][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:52.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:52.754][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:52.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:52.776][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:52.778][private$selectFields]
biodb.TRACE[2024-07-08 01:13:52.794][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 01:13:52.797][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 01:13:52.799][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:52.811][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.814][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:52.818][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:52.821][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.835][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:52.840][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:52.843][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:52.875][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:52.878][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.881][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:52.893][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:52.895][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-08 01:13:52.898][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:52.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:52.920][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:52.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:52.940][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:52.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:52.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:52.959][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-07-08 01:13:52.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:52.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:52.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:53.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:53.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:53.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:53.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:13:53.041][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.061][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.083][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:53.086][private$selectFields]
biodb.TRACE[2024-07-08 01:13:53.099][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 01:13:53.101][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 01:13:53.109][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:53.112][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.114][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.132][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.148][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.151][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.157][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.160][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:53.162][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:53.164][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.167][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.184][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.187][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-08 01:13:53.189][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.210][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.225][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.246][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-07-08 01:13:53.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:53.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:53.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:53.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:53.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:53.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:53.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:13:53.303][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.323][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.344][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:53.346][private$selectFields]
biodb.TRACE[2024-07-08 01:13:53.349][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 01:13:53.362][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 01:13:53.365][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:53.368][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.370][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.386][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.388][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.391][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.405][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.411][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:53.414][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-08 01:13:53.428][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.431][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.449][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.460][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-08 01:13:53.463][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.479][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.490][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:13:53.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:13:53.516][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-07-08 01:13:53.540][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-08 01:13:53.547][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-08 01:13:53.669][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-08 01:13:53.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-08 01:13:53.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:13:53.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-08 01:13:53.709][biodb::testThat]
biodb.INFO [2024-07-08 01:13:53.734][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-07-08 01:13:53.737][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:13:53.740][biodb::testThat]
biodb.DEBUG[2024-07-08 01:13:53.755][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-07-08 01:13:53.758][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 01:13:53.761][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-07-08 01:13:53.776][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 01:13:53.781][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 01:13:53.786][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 01:13:53.800][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-08 01:13:53.803][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 01:13:53.805][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 01:13:53.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:13:53.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:13:53.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:13:53.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:13:53.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:13:53.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:13:53.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:13:53.920][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-07-08 01:13:54.026][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:13:54.038][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:13:54.126][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-08 01:13:54.748][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:13:54.750][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:13:54.752][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[2024-07-08 01:13:54.755][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-08 01:13:55.603][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:13:55.617][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:13:55.619][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:13:55.622][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-08 01:13:56.215][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:13:56.217][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:13:56.219][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[2024-07-08 01:13:56.221][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-08 01:13:57.081][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:13:57.083][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:13:57.085][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:13:57.088][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-08 01:13:57.687][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:13:57.690][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:13:57.692][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[2024-07-08 01:13:57.695][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-08 01:13:58.459][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:13:58.461][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:13:58.464][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:13:58.467][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-08 01:13:59.065][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:13:59.072][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:13:59.075][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[2024-07-08 01:13:59.078][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-08 01:13:59.694][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:13:59.698][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:13:59.700][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:13:59.703][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-08 01:14:00.349][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:00.350][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:00.351][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[2024-07-08 01:14:00.352][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-08 01:14:01.288][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:01.291][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:01.293][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:01.296][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-08 01:14:01.918][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:01.919][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:01.921][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:14:01.923][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-08 01:14:02.696][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:02.699][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:02.701][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:03.030][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-08 01:14:03.678][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:03.679][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:03.681][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[2024-07-08 01:14:03.687][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-08 01:14:04.283][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:04.286][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:04.287][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:04.290][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-08 01:14:04.871][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:04.873][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:04.876][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[2024-07-08 01:14:04.878][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-08 01:14:05.727][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:05.733][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:05.735][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:05.738][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-08 01:14:06.332][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:06.340][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:06.343][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[2024-07-08 01:14:06.346][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-08 01:14:06.949][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:06.952][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:06.955][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:06.971][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-08 01:14:07.599][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:07.601][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:07.602][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[2024-07-08 01:14:07.603][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-08 01:14:08.165][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-07-08 01:14:08.175][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-07-08 01:14:08.178][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 01:14:08.180][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-07-08 01:14:08.181][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-08 01:14:08.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:14:08.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:08.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:08.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:08.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:08.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:08.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:14:08.227][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:14:08.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:14:08.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:08.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:08.233][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:14:08.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:14:08.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:08.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:08.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:08.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:08.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:08.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:08.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:08.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:08.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:08.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:08.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:08.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:08.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:08.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:08.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:08.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:08.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:08.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:08.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:08.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:08.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:08.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:08.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:08.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:08.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:08.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:14:08.288][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-07-08 01:14:08.289][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-07-08 01:14:08.337][biodb::testThat]
biodb.INFO [2024-07-08 01:14:08.339][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-07-08 01:14:08.342][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:14:08.345][biodb::testThat]
biodb.DEBUG[2024-07-08 01:14:08.367][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-07-08 01:14:08.374][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-07-08 01:14:08.375][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-08 01:14:08.377][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-07-08 01:14:08.379][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-07-08 01:14:08.381][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 01:14:08.382][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 01:14:08.384][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-08 01:14:08.385][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 01:14:08.386][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 01:14:08.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:14:08.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:08.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:08.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:08.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:08.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:08.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:08.476][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-07-08 01:14:08.501][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:08.503][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:08.504][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-08 01:14:09.063][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:09.067][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:09.069][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:14:09.072][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-08 01:14:09.645][private$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[2024-07-08 01:14:09.650][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:09.652][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:09.654][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-08 01:14:10.218][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:10.220][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:10.223][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:14:10.226][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-08 01:14:11.130][private$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[2024-07-08 01:14:11.132][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:11.135][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:11.138][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-08 01:14:11.704][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:11.804][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:11.807][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:14:11.814][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-08 01:14:12.612][private$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[2024-07-08 01:14:12.615][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:12.617][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:12.620][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-08 01:14:13.166][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:13.168][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:13.169][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:14:13.171][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-08 01:14:13.763][private$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[2024-07-08 01:14:13.766][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:13.768][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:13.771][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-08 01:14:14.319][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:14.321][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:14.324][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:14:14.326][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-08 01:14:14.937][private$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[2024-07-08 01:14:14.940][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:14.945][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:14.948][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-08 01:14:15.494][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:15.496][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:15.498][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:14:15.500][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-08 01:14:16.452][private$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[2024-07-08 01:14:16.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:16.457][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:16.460][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-08 01:14:17.009][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:17.012][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:17.021][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:14:17.024][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-08 01:14:17.573][private$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[2024-07-08 01:14:17.592][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:17.604][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:17.607][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-08 01:14:18.188][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:18.196][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:18.199][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:14:18.202][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-08 01:14:18.999][private$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[2024-07-08 01:14:19.001][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:19.003][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:19.005][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-08 01:14:19.545][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:19.591][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:19.592][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:14:19.594][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-08 01:14:20.139][private$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[2024-07-08 01:14:20.141][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:20.145][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:20.168][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-08 01:14:20.777][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:20.779][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:20.781][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:14:20.784][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-08 01:14:21.561][private$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[2024-07-08 01:14:21.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:14:21.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:21.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:21.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:21.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:21.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:21.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:21.596][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-07-08 01:14:21.604][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:21.607][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:21.610][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-08 01:14:22.176][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:22.202][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:22.205][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[2024-07-08 01:14:22.244][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-08 01:14:23.030][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:23.033][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:23.035][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:23.038][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-08 01:14:23.597][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:23.611][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:23.625][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[2024-07-08 01:14:23.650][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-08 01:14:24.198][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:24.212][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:24.215][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:24.229][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-08 01:14:24.809][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:24.811][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:24.824][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[2024-07-08 01:14:24.837][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-08 01:14:25.469][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:25.473][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:25.476][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:25.480][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-08 01:14:26.083][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:26.084][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:26.085][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:14:26.087][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-08 01:14:26.619][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:26.657][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:26.659][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:26.661][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-08 01:14:27.220][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:27.263][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:27.265][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[2024-07-08 01:14:27.267][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-08 01:14:27.811][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:27.829][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:27.875][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:27.902][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-08 01:14:28.508][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:28.628][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:28.630][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[2024-07-08 01:14:28.634][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-08 01:14:29.526][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:29.528][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:29.530][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:29.534][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-08 01:14:30.086][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:30.089][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:30.091][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[2024-07-08 01:14:30.095][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-08 01:14:30.923][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:30.941][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:30.946][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:30.998][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-08 01:14:31.578][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:31.581][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:31.585][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[2024-07-08 01:14:31.587][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-08 01:14:32.668][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:32.671][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:32.675][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:32.679][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-08 01:14:33.378][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:33.540][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:33.542][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[2024-07-08 01:14:33.545][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-08 01:14:34.340][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:14:34.343][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:34.345][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:34.348][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-08 01:14:34.901][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:14:34.904][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:14:34.906][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[2024-07-08 01:14:34.908][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-08 01:14:35.530][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-07-08 01:14:35.535][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-07-08 01:14:35.540][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 01:14:35.543][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-07-08 01:14:35.547][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-08 01:14:35.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:14:35.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:35.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:35.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:35.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:35.585][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:35.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:14:35.598][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:14:35.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:14:35.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:35.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:35.613][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:14:35.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:14:35.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:35.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:35.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:35.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:35.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:35.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:14:35.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:14:35.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:35.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:35.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:35.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:35.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:35.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:14:35.705][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:14:35.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:14:35.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:35.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:35.722][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:14:35.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:14:35.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:35.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:35.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:35.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:35.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:35.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:35.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:35.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:35.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:35.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:35.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:35.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:35.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:35.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:35.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:35.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:35.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:35.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:35.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:35.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:35.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:35.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:35.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:35.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:35.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:35.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:35.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:35.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:35.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:35.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:35.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:35.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:36.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:36.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:36.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:36.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:36.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:36.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:36.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:36.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:36.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:36.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:36.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:14:36.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:14:36.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:36.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:14:36.107][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-07-08 01:14:36.124][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-07-08 01:14:36.127][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-07-08 01:14:37.243][biodb::testThat]
biodb.INFO [2024-07-08 01:14:37.271][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-07-08 01:14:37.297][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:14:37.305][biodb::testThat]
biodb.INFO [2024-07-08 01:14:38.213][biodb::testThat]
biodb.INFO [2024-07-08 01:14:38.215][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-07-08 01:14:38.219][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:14:38.222][biodb::testThat]
biodb.INFO [2024-07-08 01:14:38.252][biodb::testThat]
biodb.INFO [2024-07-08 01:14:38.257][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-07-08 01:14:38.261][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:14:38.264][biodb::testThat]
biodb.DEBUG[2024-07-08 01:14:38.275][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-07-08 01:14:38.284][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:38.288][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:38.294][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-07-08 01:14:42.320][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-07-08 01:14:50.535][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 01:14:50.570][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-07-08 01:14:50.882][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-07-08 01:14:52.900][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 01:14:52.901][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 01:14:52.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:52.904][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:14:52.905][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:14:52.907][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 01:14:52.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:14:52.909][ef$get] fields variable is a list.
biodb.INFO [2024-07-08 01:14:52.911][biodb::testThat]
biodb.INFO [2024-07-08 01:14:52.913][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-07-08 01:14:52.914][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:14:52.915][biodb::testThat]
biodb.ERROR[2024-07-08 01:14:52.958][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-07-08 01:14:53.018][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-07-08 01:14:53.060][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-08 01:14:53.064][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-07-08 01:14:53.086][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-07-08 01:14:53.204][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-08 01:14:53.206][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:53.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:53.211][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:53.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:53.216][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.218][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.INFO [2024-07-08 01:14:53.264][biodb::testContext]
biodb.INFO [2024-07-08 01:14:53.266][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 01:14:53.268][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-07-08 01:14:53.271][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 01:14:53.273][biodb::testContext]
biodb.INFO [2024-07-08 01:14:53.279][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-08 01:14:53.284][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-08 01:14:53.309][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 01:14:53.312][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-08 01:14:53.316][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-08 01:14:53.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.324][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-08 01:14:53.327][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-08 01:14:53.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.562][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-08 01:14:53.565][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-08 01:14:53.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.576][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-08 01:14:53.579][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-08 01:14:53.582][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-08 01:14:53.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.594][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-08 01:14:53.596][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-08 01:14:53.599][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-08 01:14:53.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.609][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-08 01:14:53.612][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-08 01:14:53.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.621][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-08 01:14:53.624][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-08 01:14:53.627][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-08 01:14:53.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.659][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-08 01:14:53.662][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-08 01:14:53.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.672][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-08 01:14:53.675][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-08 01:14:53.678][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-08 01:14:53.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.689][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-08 01:14:53.692][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-08 01:14:53.695][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-08 01:14:53.698][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-08 01:14:53.701][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-08 01:14:53.704][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-08 01:14:53.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.714][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-08 01:14:53.717][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-08 01:14:53.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.728][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-08 01:14:53.730][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-08 01:14:53.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.742][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-08 01:14:53.746][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-08 01:14:53.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.776][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-08 01:14:53.780][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-08 01:14:53.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.791][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-08 01:14:53.793][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-08 01:14:53.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.804][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-08 01:14:53.807][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-08 01:14:53.858][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-08 01:14:53.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.869][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-08 01:14:53.871][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-08 01:14:53.874][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-08 01:14:53.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:53.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:53.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:53.927][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-08 01:14:53.933][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:53.938][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-08 01:14:53.941][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:53.944][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:14:53.946][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:53.949][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:14:53.952][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:53.955][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:14:53.958][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 01:14:53.961][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:14:54.024][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.027][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-08 01:14:54.030][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:14:54.032][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.035][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.038][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 01:14:54.038][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 01:14:54.038][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 01:14:54.038][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 01:14:54.038][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 01:14:54.041][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:14:54.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:14:54.046][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:14:54.049][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:14:54.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:14:54.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:14:54.057][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:14:54.059][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.062][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:14:54.065][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:14:54.067][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:54.070][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.073][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-08 01:14:54.077][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:54.080][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 01:14:54.082][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.084][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:14:54.087][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.090][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:14:54.092][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:54.193][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:14:54.195][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 01:14:54.198][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:14:54.200][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.203][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-08 01:14:54.206][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:14:54.208][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.210][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.213][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 01:14:54.213][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 01:14:54.213][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 01:14:54.213][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 01:14:54.213][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 01:14:54.215][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:14:54.217][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:14:54.219][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:14:54.221][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:14:54.223][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:14:54.225][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:14:54.227][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:14:54.229][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.231][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:14:54.233][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:14:54.235][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:54.236][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.238][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-08 01:14:54.240][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.241][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-08 01:14:54.243][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.245][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:14:54.247][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.249][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:14:54.252][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:54.253][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:14:54.255][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 01:14:54.256][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:14:54.257][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:54.259][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-08 01:14:54.260][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:14:54.261][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.263][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.264][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.266][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:14:54.268][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:14:54.269][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:14:54.272][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:14:54.274][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:14:54.275][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:14:54.277][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:14:54.282][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.284][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:14:54.286][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:14:54.290][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:54.293][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.296][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-08 01:14:54.298][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.300][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 01:14:54.303][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.305][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:14:54.308][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.310][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:14:54.312][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:54.314][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:14:54.316][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 01:14:54.319][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:14:54.321][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:54.323][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-08 01:14:54.325][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:14:54.328][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.330][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:54.333][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.335][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:14:54.337][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:14:54.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:14:54.341][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:14:54.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:14:54.346][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:14:54.348][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:14:54.351][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.353][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:14:54.355][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:14:54.358][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:54.360][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:54.364][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 01:14:54.366][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.460][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[2024-07-08 01:14:54.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.580][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[2024-07-08 01:14:54.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:54.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:54.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:54.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:54.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:54.593][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-08 01:14:54.599][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-08 01:14:54.603][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-08 01:14:54.609][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-08 01:14:54.612][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-08 01:14:54.615][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-08 01:14:54.619][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-08 01:14:54.623][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-08 01:14:54.626][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-08 01:14:54.656][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-08 01:14:54.659][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-08 01:14:54.663][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-08 01:14:54.666][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-08 01:14:54.670][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-08 01:14:54.673][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-08 01:14:54.676][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-08 01:14:54.680][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-08 01:14:54.683][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-08 01:14:54.704][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-08 01:14:54.708][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-08 01:14:54.713][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-08 01:14:54.717][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-08 01:14:54.722][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-08 01:14:54.726][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-08 01:14:54.731][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-08 01:14:54.735][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-08 01:14:54.739][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-08 01:14:54.743][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-08 01:14:54.748][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-08 01:14:54.752][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-08 01:14:54.756][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-08 01:14:54.761][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-08 01:14:54.765][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-08 01:14:54.769][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-08 01:14:54.772][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-08 01:14:54.776][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-08 01:14:54.779][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-08 01:14:54.783][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-08 01:14:54.787][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-08 01:14:54.790][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-08 01:14:54.794][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-08 01:14:54.798][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-08 01:14:54.802][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-08 01:14:54.806][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-08 01:14:54.809][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-08 01:14:54.817][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-08 01:14:54.821][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-08 01:14:54.825][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-08 01:14:54.830][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-08 01:14:54.836][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-08 01:14:54.843][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-08 01:14:54.849][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-08 01:14:54.855][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-08 01:14:54.876][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-08 01:14:54.882][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-08 01:14:54.904][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-08 01:14:54.908][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-08 01:14:54.912][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-08 01:14:54.916][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-08 01:14:54.920][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-08 01:14:54.924][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-08 01:14:54.928][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-08 01:14:54.932][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-08 01:14:54.936][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-08 01:14:54.939][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-08 01:14:54.943][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-08 01:14:54.947][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-08 01:14:54.950][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-08 01:14:54.954][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-08 01:14:54.958][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-08 01:14:54.961][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-08 01:14:54.964][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-08 01:14:54.968][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-08 01:14:54.971][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-08 01:14:54.976][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-08 01:14:54.980][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-08 01:14:54.985][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-08 01:14:54.989][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-08 01:14:54.996][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-08 01:14:55.000][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-08 01:14:55.003][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-08 01:14:55.007][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-08 01:14:55.010][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-08 01:14:55.014][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-08 01:14:55.018][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-08 01:14:55.036][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 01:14:55.040][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.046][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.082][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[2024-07-08 01:14:55.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:14:55.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:14:55.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:14:55.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:14:55.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:14:55.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:14:55.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:14:55.378][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-07-08 01:14:55.382][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-07-08 01:14:55.387][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:55.389][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-08 01:14:55.392][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:55.395][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:14:55.412][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:55.415][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:14:55.418][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:55.420][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:14:55.423][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 01:14:55.425][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:14:55.427][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:55.429][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-07-08 01:14:55.430][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:14:55.432][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-07-08 01:14:55.432][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-07-08 01:14:55.432][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-07-08 01:14:55.432][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-07-08 01:14:55.432][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-07-08 01:14:55.432][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-07-08 01:14:55.432][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-07-08 01:14:55.432][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-07-08 01:14:55.432][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-07-08 01:14:55.435][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-08 01:14:55.437][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 01:14:55.437][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 01:14:55.440][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:14:55.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:14:55.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:14:55.447][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:14:55.449][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:14:55.451][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:14:55.453][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:14:55.456][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-08 01:14:55.456][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-07-08 01:14:55.458][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:14:55.460][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:14:55.463][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-08 01:14:55.465][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:14:55.469][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-07-08 01:14:55.474][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-08 01:14:55.485][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-07-08 01:14:55.488][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-07-08 01:14:55.493][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-07-08 01:14:55.497][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-07-08 01:14:55.507][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-08 01:14:55.510][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-08 01:14:55.514][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-07-08 01:14:55.520][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-07-08 01:14:55.525][biodb::testThat]
biodb.INFO [2024-07-08 01:14:55.528][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-07-08 01:14:55.531][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:14:55.533][biodb::testThat]
biodb.DEBUG[2024-07-08 01:14:55.543][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[2024-07-08 01:14:55.557][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:55.560][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:55.563][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-07-08 01:14:56.178][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-07-08 01:14:56.801][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 01:14:56.810][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-07-08 01:14:56.822][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-07-08 01:14:56.884][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-07-08 01:14:56.893][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:56.896][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:56.901][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-07-08 01:14:57.518][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[2024-07-08 01:14:58.135][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 01:14:58.139][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-07-08 01:14:58.321][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-07-08 01:14:58.347][biodb::testThat]
biodb.INFO [2024-07-08 01:14:58.349][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-07-08 01:14:58.352][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:14:58.354][biodb::testThat]
biodb.INFO [2024-07-08 01:14:58.481][biodb::testThat]
biodb.INFO [2024-07-08 01:14:58.484][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-07-08 01:14:58.487][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:14:58.489][biodb::testThat]
biodb.DEBUG[2024-07-08 01:14:58.497][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[2024-07-08 01:14:58.505][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:58.508][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:14:58.513][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-07-08 01:14:58.966][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-07-08 01:14:59.406][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 01:14:59.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-07-08 01:14:59.437][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-07-08 01:14:59.448][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-07-08 01:14:59.456][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 01:14:59.459][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-07-08 01:14:59.462][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 01:14:59.465][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-07-08 01:14:59.479][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-07-08 01:14:59.487][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:14:59.489][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-08 01:14:59.492][rule$waitAsNeeded] Wait 0.0196431 second(s).
biodb.TRACE[2024-07-08 01:14:59.523][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-07-08 01:14:59.979][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-07-08 01:15:00.429][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 01:15:00.453][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-07-08 01:15:00.474][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-07-08 01:15:00.490][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-07-08 01:15:00.497][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:00.500][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-08 01:15:00.502][rule$waitAsNeeded] Wait 0.0195861 second(s).
biodb.TRACE[2024-07-08 01:15:00.656][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-07-08 01:15:01.871][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-07-08 01:15:03.374][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 01:15:03.384][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-07-08 01:15:03.427][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-07-08 01:15:03.714][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-07-08 01:15:03.723][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:03.726][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:03.731][private$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[2024-07-08 01:15:05.064][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[2024-07-08 01:15:06.555][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 01:15:06.561][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-07-08 01:15:06.659][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-07-08 01:15:06.973][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-08 01:15:06.976][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-07-08 01:15:06.979][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-07-08 01:15:06.981][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-08 01:15:06.983][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:06.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:06.987][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:06.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:06.992][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:06.994][FUN] Functions in observer BiodbConfig: [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 [2024-07-08 01:15:07.004][biodb::testContext]
biodb.INFO [2024-07-08 01:15:07.006][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 01:15:07.008][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-07-08 01:15:07.012][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 01:15:07.035][biodb::testContext]
biodb.INFO [2024-07-08 01:15:07.040][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-08 01:15:07.044][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-08 01:15:07.056][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 01:15:07.058][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-08 01:15:07.061][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-08 01:15:07.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.072][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-08 01:15:07.074][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-08 01:15:07.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.086][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-08 01:15:07.089][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-08 01:15:07.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.098][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-08 01:15:07.100][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-08 01:15:07.103][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-08 01:15:07.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.111][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-08 01:15:07.121][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-08 01:15:07.124][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-08 01:15:07.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.134][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-08 01:15:07.137][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-08 01:15:07.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.150][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-08 01:15:07.152][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-08 01:15:07.155][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-08 01:15:07.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.169][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-08 01:15:07.172][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-08 01:15:07.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.181][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-08 01:15:07.183][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-08 01:15:07.185][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-08 01:15:07.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.193][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-08 01:15:07.196][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-08 01:15:07.198][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-08 01:15:07.201][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-08 01:15:07.203][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-08 01:15:07.207][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-08 01:15:07.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.217][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-08 01:15:07.220][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-08 01:15:07.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.230][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-08 01:15:07.232][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-08 01:15:07.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.242][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-08 01:15:07.245][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-08 01:15:07.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.257][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-08 01:15:07.260][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-08 01:15:07.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.289][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-08 01:15:07.291][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-08 01:15:07.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.324][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-08 01:15:07.328][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-08 01:15:07.348][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-08 01:15:07.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.359][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-08 01:15:07.362][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-08 01:15:07.364][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-08 01:15:07.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.375][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-08 01:15:07.379][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:07.382][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-08 01:15:07.385][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.388][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:15:07.390][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.393][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:15:07.399][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:07.402][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:15:07.404][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 01:15:07.407][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:15:07.409][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.412][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-08 01:15:07.414][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:15:07.417][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.419][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.422][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 01:15:07.422][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 01:15:07.422][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 01:15:07.422][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 01:15:07.422][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 01:15:07.425][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:15:07.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:15:07.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:15:07.432][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:15:07.435][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:15:07.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:15:07.439][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:15:07.442][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.445][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:15:07.526][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:15:07.528][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:07.532][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.536][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-08 01:15:07.540][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:07.542][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 01:15:07.545][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.548][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:15:07.551][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.554][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:15:07.557][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:07.560][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:15:07.564][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 01:15:07.567][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:15:07.574][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.577][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-08 01:15:07.605][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:15:07.608][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.611][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.614][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 01:15:07.614][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 01:15:07.614][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 01:15:07.614][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 01:15:07.614][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 01:15:07.616][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:15:07.619][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:15:07.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:15:07.624][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:15:07.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:15:07.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:15:07.631][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:15:07.634][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.637][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:15:07.639][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:15:07.642][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:07.646][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.649][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-08 01:15:07.654][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.657][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-08 01:15:07.660][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.662][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:15:07.666][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.669][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:15:07.672][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:07.675][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:15:07.678][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 01:15:07.698][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:15:07.701][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:07.706][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-08 01:15:07.709][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:15:07.711][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.714][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.718][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.720][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:15:07.723][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:15:07.725][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:15:07.728][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:15:07.731][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:15:07.734][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:15:07.737][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:15:07.739][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.742][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:15:07.744][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:15:07.748][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:07.751][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.754][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-08 01:15:07.759][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.761][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 01:15:07.764][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.766][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:15:07.769][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.771][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:15:07.774][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:07.776][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:15:07.780][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 01:15:07.783][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:15:07.786][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:07.789][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-08 01:15:07.793][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:15:07.796][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.798][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:07.800][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.805][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:15:07.808][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:15:07.810][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:15:07.816][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:15:07.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:15:07.821][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:15:07.823][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:15:07.826][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.828][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:15:07.830][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:15:07.833][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:07.836][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:07.839][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 01:15:07.842][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:07.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:07.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:07.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:07.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:07.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:07.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:07.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:07.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:07.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:07.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.954][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[2024-07-08 01:15:07.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:07.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:07.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:07.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:07.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:07.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:07.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:07.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:07.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:07.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.024][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[2024-07-08 01:15:08.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.047][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[2024-07-08 01:15:08.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.139][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-08 01:15:08.143][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-08 01:15:08.147][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-08 01:15:08.152][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-08 01:15:08.156][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-08 01:15:08.159][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-08 01:15:08.163][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-08 01:15:08.167][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-08 01:15:08.171][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-08 01:15:08.175][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-08 01:15:08.180][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-08 01:15:08.183][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-08 01:15:08.187][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-08 01:15:08.191][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-08 01:15:08.196][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-08 01:15:08.200][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-08 01:15:08.207][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-08 01:15:08.211][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-08 01:15:08.222][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-08 01:15:08.243][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-08 01:15:08.247][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-08 01:15:08.251][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-08 01:15:08.255][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-08 01:15:08.259][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-08 01:15:08.262][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-08 01:15:08.265][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-08 01:15:08.269][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-08 01:15:08.273][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-08 01:15:08.276][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-08 01:15:08.280][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-08 01:15:08.352][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-08 01:15:08.356][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-08 01:15:08.360][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-08 01:15:08.364][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-08 01:15:08.367][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-08 01:15:08.371][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-08 01:15:08.374][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-08 01:15:08.377][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-08 01:15:08.384][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-08 01:15:08.387][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-08 01:15:08.391][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-08 01:15:08.432][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-08 01:15:08.438][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-08 01:15:08.442][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-08 01:15:08.446][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-08 01:15:08.450][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-08 01:15:08.457][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-08 01:15:08.510][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-08 01:15:08.515][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-08 01:15:08.519][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-08 01:15:08.522][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-08 01:15:08.525][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-08 01:15:08.529][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-08 01:15:08.537][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-08 01:15:08.541][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-08 01:15:08.597][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-08 01:15:08.601][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-08 01:15:08.605][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-08 01:15:08.608][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-08 01:15:08.612][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-08 01:15:08.633][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-08 01:15:08.637][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-08 01:15:08.642][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-08 01:15:08.645][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-08 01:15:08.654][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-08 01:15:08.708][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-08 01:15:08.712][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-08 01:15:08.716][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-08 01:15:08.720][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-08 01:15:08.724][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-08 01:15:08.728][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-08 01:15:08.732][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-08 01:15:08.735][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-08 01:15:08.737][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-08 01:15:08.746][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-08 01:15:08.749][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-08 01:15:08.753][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-08 01:15:08.756][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-08 01:15:08.760][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-08 01:15:08.764][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-08 01:15:08.771][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-08 01:15:08.775][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-08 01:15:08.787][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-08 01:15:08.791][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-08 01:15:08.797][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-08 01:15:08.800][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 01:15:08.802][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.806][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:08.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:08.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:08.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:08.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:08.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:08.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:08.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:08.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:08.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:08.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:08.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:08.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:08.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:08.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:08.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:08.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:08.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:08.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:08.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:09.003][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[2024-07-08 01:15:09.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:09.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:09.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:09.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:09.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:09.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:09.024][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[2024-07-08 01:15:09.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:09.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:09.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:09.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:09.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:09.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:09.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:09.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:09.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:09.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:09.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:09.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:09.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:09.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:09.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:09.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:09.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:09.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:09.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:09.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:09.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:09.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:09.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:09.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:09.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:09.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:09.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:09.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:09.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:09.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:09.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:09.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:09.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:09.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:09.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:09.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:09.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:09.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:09.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:09.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:09.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:09.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:09.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:09.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:09.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:09.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:09.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:09.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:09.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:09.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:09.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:09.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:09.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:09.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:09.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:09.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:09.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 01:15:09.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:09.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:09.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:09.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:09.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:09.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:09.195][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-07-08 01:15:09.199][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-07-08 01:15:09.203][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:09.206][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-08 01:15:09.209][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:09.211][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 01:15:09.214][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:09.216][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 01:15:09.218][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:09.222][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 01:15:09.225][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 01:15:09.227][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 01:15:09.230][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:09.233][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-07-08 01:15:09.243][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 01:15:09.246][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-07-08 01:15:09.246][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-07-08 01:15:09.246][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-07-08 01:15:09.246][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-07-08 01:15:09.246][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-07-08 01:15:09.246][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-07-08 01:15:09.246][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-07-08 01:15:09.246][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-07-08 01:15:09.246][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-07-08 01:15:09.260][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-08 01:15:09.262][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 01:15:09.262][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 01:15:09.265][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 01:15:09.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:15:09.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:15:09.275][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 01:15:09.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 01:15:09.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 01:15:09.281][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 01:15:09.284][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-08 01:15:09.284][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-07-08 01:15:09.286][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 01:15:09.288][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 01:15:09.291][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-08 01:15:09.293][self$setPropertyValue]
biodb.DEBUG[2024-07-08 01:15:09.297][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-07-08 01:15:09.300][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-08 01:15:09.308][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-07-08 01:15:09.311][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-07-08 01:15:09.314][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-07-08 01:15:09.317][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-07-08 01:15:09.320][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-08 01:15:09.323][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-08 01:15:09.326][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-07-08 01:15:09.331][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-07-08 01:15:09.334][biodb::testThat]
biodb.INFO [2024-07-08 01:15:09.351][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-07-08 01:15:09.354][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 01:15:09.356][biodb::testThat]
biodb.DEBUG[2024-07-08 01:15:09.365][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[2024-07-08 01:15:09.373][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 01:15:09.379][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-07-08 01:15:09.382][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 01:15:09.555][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-07-08 01:15:11.504][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-07-08 01:15:11.545][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-08 01:15:11.550][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-07-08 01:15:11.553][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-07-08 01:15:11.556][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 01:15:11.559][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 01:15:11.561][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-08 01:15:11.564][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 01:15:11.568][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 01:15:11.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:15:11.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:11.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:11.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:11.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:11.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:11.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:11.722][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-07-08 01:15:11.729][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:11.732][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:11.735][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-07-08 01:15:12.287][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:12.290][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:12.292][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:12.294][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-07-08 01:15:13.166][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:13.178][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:13.223][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:13.227][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-07-08 01:15:13.777][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:13.780][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:13.782][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:13.784][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-07-08 01:15:14.341][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:14.343][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:14.354][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:14.357][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-07-08 01:15:14.914][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:14.917][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:14.919][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:14.922][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-07-08 01:15:15.587][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:15.595][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:15.598][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:15.602][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-07-08 01:15:16.153][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:16.154][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:16.156][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:16.159][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-07-08 01:15:17.156][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:17.158][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:17.160][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:17.163][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-07-08 01:15:17.712][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:17.714][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:17.716][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:17.719][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-07-08 01:15:18.403][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:18.405][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:18.408][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:18.411][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-07-08 01:15:18.959][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:18.961][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:18.964][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:18.967][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-07-08 01:15:19.748][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:19.765][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:19.767][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:19.771][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-07-08 01:15:20.323][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:20.325][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:20.326][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:20.329][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-07-08 01:15:20.880][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:20.882][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:20.884][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:20.887][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-07-08 01:15:21.438][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:21.440][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:21.443][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:21.445][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-07-08 01:15:22.667][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:22.670][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:22.673][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:22.677][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-07-08 01:15:23.235][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:23.240][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:23.243][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:23.245][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-07-08 01:15:23.894][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:23.897][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:23.899][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:23.902][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-07-08 01:15:24.459][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:24.461][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:24.464][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:24.466][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-07-08 01:15:25.002][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:25.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:15:25.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:25.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:25.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:25.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:25.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:25.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 01:15:25.037][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-07-08 01:15:25.045][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:25.048][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:25.052][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-07-08 01:15:25.608][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:25.610][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:25.612][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:25.615][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-07-08 01:15:26.383][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:26.387][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:26.389][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:26.393][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-07-08 01:15:26.946][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:26.948][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:26.951][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:26.953][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-07-08 01:15:27.607][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:27.610][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:27.613][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:27.616][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-07-08 01:15:28.170][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:28.172][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:28.174][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:28.176][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-07-08 01:15:28.937][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:28.940][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:28.942][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:28.945][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-07-08 01:15:29.502][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:29.521][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:29.524][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:29.526][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-07-08 01:15:30.293][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:30.295][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:30.298][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:30.301][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-07-08 01:15:30.854][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:30.857][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:30.871][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:30.874][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-07-08 01:15:31.661][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:31.663][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:31.666][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:31.675][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-07-08 01:15:32.226][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:32.229][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:32.231][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:32.234][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-07-08 01:15:32.785][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:32.788][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:32.791][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:32.795][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-07-08 01:15:33.347][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:33.354][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:33.382][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:33.385][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-07-08 01:15:33.934][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:33.939][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:33.970][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:33.975][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-07-08 01:15:34.532][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:34.534][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:34.537][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:34.540][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-07-08 01:15:35.542][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:35.544][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:35.547][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:35.550][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-07-08 01:15:36.105][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:36.122][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:36.124][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:36.125][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-07-08 01:15:36.629][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-08 01:15:36.631][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 01:15:36.633][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 01:15:36.636][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-07-08 01:15:37.168][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-07-08 01:15:37.171][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-08 01:15:37.173][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-08 01:15:37.176][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-07-08 01:15:38.006][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.TRACE[2024-07-08 01:15:38.012][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv"
biodb.DEBUG[2024-07-08 01:15:38.017][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 01:15:38.020][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-07-08 01:15:38.023][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-08 01:15:38.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:15:38.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:38.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:38.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:38.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:38.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:38.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:15:38.054][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:15:38.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:15:38.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.080][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:15:38.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:15:38.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:15:38.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:15:38.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:15:38.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:15:38.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:38.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:38.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:38.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:38.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:38.215][FUN] Functions in observer BiodbConfig: [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[2024-07-08 01:15:38.272][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:15:38.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:15:38.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.283][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:15:38.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-08 01:15:38.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:15:38.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:15:38.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:15:38.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:15:38.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:15:38.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:15:38.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:15:38.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:15:38.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:15:38.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:15:38.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:15:38.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:15:38.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:15:38.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:15:38.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:15:38.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:15:38.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:15:38.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:15:38.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:15:38.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:15:38.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 01:15:38.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 01:15:38.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 01:15:38.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 01:15:38.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 01:15:38.456][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-07-08 01:15:38.458][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-07-08 01:15:38.465][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-08 01:15:38.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:15:38.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:38.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:38.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:38.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:38.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:38.492][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.TRACE[2024-07-08 01:15:38.495][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-07-08 01:15:38.498][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 01:15:38.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:38.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:38.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:38.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:38.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:38.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 01:15:38.524][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-07-08 01:15:38.527][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-07-08 01:15:38.529][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-07-08 01:15:38.549][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-08 01:15:38.583][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-07-08 01:15:38.586][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-07-08 01:15:38.589][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-08 01:15:38.591][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 01:15:38.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 01:15:38.596][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 01:15:38.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 01:15:38.602][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 01:15:38.605][FUN] Functions in observer 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
LipidmapsStructureConn 4.390 1.24611.548
LipidmapsStructureEntry0.8480.0231.835