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This page was generated on 2024-04-17 11:37:32 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 200/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_18
git_last_commit: f02eedd
git_last_commit_date: 2023-10-24 11:38:15 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for biodbLipidmaps on 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: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.8.0.tar.gz
StartedAt: 2024-04-15 23:55:02 -0400 (Mon, 15 Apr 2024)
EndedAt: 2024-04-15 23:58:47 -0400 (Mon, 15 Apr 2024)
EllapsedTime: 225.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
LipidmapsStructureConn 3.744  1.146    5.34
* 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 14 | WARN 0 | SKIP 0 | PASS 101 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

Installation output

biodbLipidmaps.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-04-15 23:56:41.173][biodb::testContext]
biodb.INFO [2024-04-15 23:56:41.180][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:56:41.182][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-04-15 23:56:41.184][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:56:41.187][biodb::testContext]
biodb.INFO [2024-04-15 23:56:41.201][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:56:41.245][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 23:56:41.261][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:56:41.264][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 23:56:41.266][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 23:56:41.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.276][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 23:56:41.329][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 23:56:41.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.338][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 23:56:41.341][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 23:56:41.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.351][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 23:56:41.354][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 23:56:41.357][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 23:56:41.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.367][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 23:56:41.369][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 23:56:41.372][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 23:56:41.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.382][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 23:56:41.385][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 23:56:41.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.392][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[2024-04-15 23:56:41.395][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 23:56:41.398][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 23:56:41.401][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 23:56:41.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.411][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 23:56:41.414][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 23:56:41.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.422][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 23:56:41.424][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 23:56:41.427][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 23:56:41.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.435][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:56:41.437][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 23:56:41.439][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 23:56:41.441][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 23:56:41.444][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 23:56:41.446][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 23:56:41.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.455][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 23:56:41.458][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 23:56:41.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.467][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 23:56:41.469][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 23:56:41.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.478][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 23:56:41.481][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 23:56:41.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.489][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 23:56:41.492][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 23:56:41.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.502][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 23:56:41.505][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 23:56:41.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.514][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:56:41.516][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 23:56:41.534][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 23:56:41.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.543][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 23:56:41.546][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 23:56:41.548][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 23:56:41.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.564][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 23:56:41.654][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:41.696][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 23:56:41.699][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.702][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:56:41.704][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.707][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:56:41.710][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:41.712][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:56:41.715][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:56:41.718][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:56:41.721][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.723][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 23:56:41.726][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:56:41.729][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.732][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.734][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:56:41.734][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:56:41.734][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:56:41.734][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:56:41.734][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:56:41.737][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:56:41.739][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:41.741][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:41.744][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:56:41.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:41.749][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:41.751][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:56:41.754][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:56:41.768][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:56:41.770][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:41.772][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.774][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 23:56:41.778][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:41.780][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:56:41.782][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.784][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:56:41.786][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.789][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:56:41.791][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:41.793][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:56:41.794][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:56:41.796][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:56:41.798][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.801][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 23:56:41.803][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:56:41.805][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.807][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.809][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:56:41.809][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:56:41.809][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:56:41.809][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:56:41.809][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:56:41.811][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:56:41.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:41.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:41.817][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:56:41.819][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:41.821][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:41.823][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:56:41.825][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.827][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:56:41.829][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:56:41.831][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:41.833][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.835][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 23:56:41.839][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.841][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 23:56:41.843][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.845][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:56:41.847][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.849][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:56:41.851][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:41.853][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:56:41.855][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:56:41.858][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:56:41.860][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:41.862][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 23:56:41.864][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:56:41.866][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.868][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.871][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.872][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:56:41.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:41.876][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:41.878][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:56:41.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:41.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:41.884][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:56:41.886][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.888][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:56:41.890][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:56:41.891][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:41.893][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.896][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 23:56:41.899][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.902][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:56:41.904][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.906][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:56:41.908][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.910][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:56:41.913][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:41.915][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:56:41.917][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:56:41.920][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:56:41.922][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:41.925][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 23:56:41.927][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:56:41.930][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.932][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:41.934][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.937][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:56:41.939][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:41.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:41.943][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:56:41.945][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:41.947][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:41.949][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:56:41.952][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.954][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:56:41.956][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:56:41.958][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:41.961][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:41.968][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:56:41.970][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:41.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:41.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:41.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:41.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:41.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:41.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:41.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:41.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:41.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.036][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[2024-04-15 23:56:42.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.056][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[2024-04-15 23:56:42.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.066][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[2024-04-15 23:56:42.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.138][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 23:56:42.148][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 23:56:42.151][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 23:56:42.154][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 23:56:42.157][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 23:56:42.161][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 23:56:42.164][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 23:56:42.168][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 23:56:42.171][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 23:56:42.174][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 23:56:42.178][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 23:56:42.181][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 23:56:42.184][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 23:56:42.188][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 23:56:42.191][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 23:56:42.194][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 23:56:42.198][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 23:56:42.201][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 23:56:42.204][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 23:56:42.208][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 23:56:42.211][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 23:56:42.214][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 23:56:42.218][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 23:56:42.221][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 23:56:42.224][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 23:56:42.228][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 23:56:42.231][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 23:56:42.234][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 23:56:42.237][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 23:56:42.241][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 23:56:42.244][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 23:56:42.247][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 23:56:42.250][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 23:56:42.254][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 23:56:42.257][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 23:56:42.261][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 23:56:42.264][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 23:56:42.267][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 23:56:42.271][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 23:56:42.274][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 23:56:42.277][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 23:56:42.281][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 23:56:42.284][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 23:56:42.288][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 23:56:42.291][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 23:56:42.294][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 23:56:42.298][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 23:56:42.301][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 23:56:42.304][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 23:56:42.308][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 23:56:42.311][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 23:56:42.314][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 23:56:42.318][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 23:56:42.321][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 23:56:42.324][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 23:56:42.328][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 23:56:42.331][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 23:56:42.335][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 23:56:42.338][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 23:56:42.342][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 23:56:42.346][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 23:56:42.350][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 23:56:42.354][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 23:56:42.358][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 23:56:42.362][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 23:56:42.375][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 23:56:42.379][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 23:56:42.383][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 23:56:42.388][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 23:56:42.391][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 23:56:42.395][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 23:56:42.398][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 23:56:42.402][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 23:56:42.405][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 23:56:42.410][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 23:56:42.414][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 23:56:42.419][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 23:56:42.422][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 23:56:42.426][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 23:56:42.429][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 23:56:42.433][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 23:56:42.437][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 23:56:42.440][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 23:56:42.454][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 23:56:42.458][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:56:42.464][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:56:42.466][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.470][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.589][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.DEBUG[2024-04-15 23:56:42.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:42.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:42.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:42.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:42.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:42.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:42.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:42.752][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-04-15 23:56:42.776][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 23:56:42.781][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:42.784][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 23:56:42.786][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:42.788][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:56:42.790][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:42.792][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:56:42.795][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:42.797][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:56:42.799][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:56:42.801][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:56:42.803][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:42.805][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-04-15 23:56:42.808][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:56:42.811][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-04-15 23:56:42.811][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-04-15 23:56:42.811][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-04-15 23:56:42.811][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-04-15 23:56:42.811][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-04-15 23:56:42.811][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-04-15 23:56:42.811][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-04-15 23:56:42.811][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-04-15 23:56:42.811][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-04-15 23:56:42.814][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:42.816][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:56:42.816][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:56:42.819][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:56:42.821][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:42.823][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:42.825][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:56:42.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:42.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:42.831][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:56:42.835][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 23:56:42.835][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-04-15 23:56:42.837][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:56:42.839][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:56:42.841][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:42.843][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:42.857][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-04-15 23:56:42.861][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 23:56:42.921][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 23:56:42.923][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-04-15 23:56:42.931][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 23:56:42.940][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-04-15 23:56:42.950][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 23:56:42.954][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 23:56:42.957][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-04-15 23:56:42.960][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-04-15 23:56:42.981][biodb::testThat]
biodb.INFO [2024-04-15 23:56:42.983][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-04-15 23:56:42.985][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:42.987][biodb::testThat]
biodb.TRACE[2024-04-15 23:56:42.999][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-04-15 23:56:43.003][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:56:43.011][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 23:56:43.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:56:43.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:43.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:43.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:43.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:43.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:43.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:56:43.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:56:43.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:56:43.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.164][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 23:56:43.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 23:56:43.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.174][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:56:43.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:56:43.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.183][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:43.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:43.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.257][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:43.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:43.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.267][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.277][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.286][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 23:56:43.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:43.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.296][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 23:56:43.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:43.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.304][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:56:43.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:56:43.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.313][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:56:43.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:56:43.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.330][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.338][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 23:56:43.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.346][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-15 23:56:43.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.362][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.371][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 23:56:43.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.431][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.523][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.532][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.541][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.562][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:56:43.628][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-04-15 23:56:43.633][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 23:56:43.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 23:56:43.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.641][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 23:56:43.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 23:56:43.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.647][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-15 23:56:43.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-15 23:56:43.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.655][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-15 23:56:43.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-15 23:56:43.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.732][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.804][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.812][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.820][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:43.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.869][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.871][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.875][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:43.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:43.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.914][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.929][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.931][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.935][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.938][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:43.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:43.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.963][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.971][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.978][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.987][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.989][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:43.993][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:43.996][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:43.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:44.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.023][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:56:44.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:56:44.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:56:44.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:56:44.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.041][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:56:44.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:56:44.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.050][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:56:44.052][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:56:44.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.056][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.058][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:56:44.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:56:44.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:44.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:44.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:44.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:44.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:44.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:44.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.139][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:44.141][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:44.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.146][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:44.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:44.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.172][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:44.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:44.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.180][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:44.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:44.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.188][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:44.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:44.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.197][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:44.199][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:44.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.203][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.205][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:44.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:44.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.232][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:44.235][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:44.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.239][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.249][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:44.252][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 23:56:44.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.256][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.266][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:56:44.269][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:56:44.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.273][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.283][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:44.286][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:44.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.290][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.302][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:44.304][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:44.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.309][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.320][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:44.322][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 23:56:44.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.327][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 23:56:44.344][biodb::testThat]
biodb.INFO [2024-04-15 23:56:44.346][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-04-15 23:56:44.348][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:44.350][biodb::testThat]
biodb.DEBUG[2024-04-15 23:56:44.382][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-04-15 23:56:44.396][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:56:44.403][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-04-15 23:56:44.405][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:56:44.409][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-04-15 23:56:44.412][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:56:44.467][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:56:44.469][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 23:56:44.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:56:44.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:44.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:44.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:44.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:44.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:44.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:56:44.497][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:44.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:44.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.506][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:44.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:56:44.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:44.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:44.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:44.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:44.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:44.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:44.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:44.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:44.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:44.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:44.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:44.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:56:44.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:56:44.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:56:44.568][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-04-15 23:56:44.571][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-04-15 23:56:44.612][biodb::testThat]
biodb.INFO [2024-04-15 23:56:44.614][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-04-15 23:56:44.616][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:44.618][biodb::testThat]
biodb.TRACE[2024-04-15 23:56:44.625][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:44.627][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:44.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:44.632][ef$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:56:44.634][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.INFO [2024-04-15 23:56:45.036][biodb::testThat]
biodb.INFO [2024-04-15 23:56:45.038][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-04-15 23:56:45.041][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:45.044][biodb::testThat]
biodb.INFO [2024-04-15 23:56:45.149][biodb::testThat]
biodb.INFO [2024-04-15 23:56:45.151][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-04-15 23:56:45.154][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:45.156][biodb::testThat]
biodb.INFO [2024-04-15 23:56:45.295][biodb::testThat]
biodb.INFO [2024-04-15 23:56:45.297][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-04-15 23:56:45.299][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:45.301][biodb::testThat]
biodb.INFO [2024-04-15 23:56:45.319][biodb::testThat]
biodb.INFO [2024-04-15 23:56:45.321][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-04-15 23:56:45.323][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:45.325][biodb::testThat]
biodb.INFO [2024-04-15 23:56:45.342][biodb::testThat]
biodb.INFO [2024-04-15 23:56:45.344][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-04-15 23:56:45.346][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:45.348][biodb::testThat]
biodb.DEBUG[2024-04-15 23:56:45.356][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-04-15 23:56:52.808][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-04-15 23:56:53.241][biodb::testThat]
biodb.INFO [2024-04-15 23:56:53.244][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-04-15 23:56:53.247][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:53.249][biodb::testThat]
biodb.TRACE[2024-04-15 23:56:53.296][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:56:53.298][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:56:53.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:53.303][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:56:53.305][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:53.307][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:56:53.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:56:53.312][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 23:56:53.315][biodb::testThat]
biodb.INFO [2024-04-15 23:56:53.318][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-04-15 23:56:53.320][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:53.322][biodb::testThat]
biodb.INFO [2024-04-15 23:56:53.426][biodb::testThat]
biodb.INFO [2024-04-15 23:56:53.428][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-04-15 23:56:53.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:53.432][biodb::testThat]
biodb.INFO [2024-04-15 23:56:53.494][biodb::testThat]
biodb.INFO [2024-04-15 23:56:53.496][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-04-15 23:56:53.499][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:53.501][biodb::testThat]
biodb.INFO [2024-04-15 23:56:53.540][biodb::testThat]
biodb.INFO [2024-04-15 23:56:53.542][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-04-15 23:56:53.545][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:53.547][biodb::testThat]
biodb.INFO [2024-04-15 23:56:53.585][biodb::testThat]
biodb.INFO [2024-04-15 23:56:53.587][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-04-15 23:56:53.590][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:56:53.592][biodb::testThat]
biodb.DEBUG[2024-04-15 23:56:53.596][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-04-15 23:56:53.719][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:56:53.758][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-04-15 23:56:53.761][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:56:53.764][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:56:53.766][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:56:53.768][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 23:56:53.770][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:56:53.772][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:56:53.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:56:53.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:56:53.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:56:53.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:53.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:53.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:53.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:53.807][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-04-15 23:56:53.856][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:56:53.859][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:56:53.861][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 23:56:54.435][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:56:54.437][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:56:54.439][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:56:54.441][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 23:56:55.040][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:56:55.043][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:56:55.045][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:56:55.082][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 23:56:55.675][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:56:55.677][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:56:55.679][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:56:55.682][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 23:56:56.468][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:56:56.470][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:56:56.479][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:56:56.488][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 23:56:57.095][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:56:57.097][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:56:57.100][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:56:57.102][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 23:56:57.979][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:56:57.982][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:56:57.984][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:56:57.987][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 23:56:58.574][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:56:58.576][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:56:58.578][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:56:58.581][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 23:56:59.176][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:56:59.178][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:56:59.180][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:56:59.183][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 23:56:59.772][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:56:59.774][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:56:59.776][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:56:59.779][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 23:57:00.564][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:00.566][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:00.568][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:00.571][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 23:57:01.157][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:01.161][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:01.164][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:01.166][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 23:57:02.076][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:02.079][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:02.102][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:02.105][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 23:57:02.697][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:02.699][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:02.701][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:02.703][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 23:57:03.619][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:03.621][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:03.623][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:03.626][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 23:57:04.225][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:04.227][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:04.229][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:04.232][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 23:57:04.925][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:04.927][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:04.929][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:04.932][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 23:57:05.516][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:05.518][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:05.520][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:05.522][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 23:57:06.449][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:06.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:06.454][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:06.457][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-04-15 23:57:07.052][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:07.089][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:07.093][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:07.096][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-04-15 23:57:07.986][private$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.INFO [2024-04-15 23:57:07.991][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-04-15 23:57:07.994][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-04-15 23:57:07.999][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:08.002][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:08.005][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 23:57:08.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:08.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:08.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:08.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:08.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:08.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:08.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:08.035][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:08.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:08.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.043][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:08.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:08.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:08.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:08.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:08.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:08.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:08.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:08.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:08.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:08.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:08.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:08.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:08.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:08.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:08.162][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-04-15 23:57:08.164][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-04-15 23:57:08.202][biodb::testThat]
biodb.INFO [2024-04-15 23:57:08.204][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-04-15 23:57:08.206][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:08.208][biodb::testThat]
biodb.DEBUG[2024-04-15 23:57:08.231][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-04-15 23:57:08.234][private$loadEntries] Creating entries from ids [3]: "WRONGB, LMFA00000002, LMFA08040013".
biodb.DEBUG[2024-04-15 23:57:08.236][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 3 id(s)...
biodb.TRACE[2024-04-15 23:57:08.239][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, LMFA00000002, LMFA08040013".
biodb.TRACE[2024-04-15 23:57:08.242][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-04-15 23:57:08.248][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:08.251][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:08.281][conn$getEntryContent] 3 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 23:57:08.283][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:08.285][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:08.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:08.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:08.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:08.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:08.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:08.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:08.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:08.408][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-04-15 23:57:08.453][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:08.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:08.460][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 23:57:09.011][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:09.014][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:09.018][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:09.020][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 23:57:09.801][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:09.813][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:09.856][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:09.860][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 23:57:10.409][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:10.411][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:10.413][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:10.415][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 23:57:11.225][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:11.227][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:11.229][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:11.232][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 23:57:11.783][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:11.785][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:11.787][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:11.790][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 23:57:12.535][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:12.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:12.542][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:12.544][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 23:57:13.090][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:13.099][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:13.141][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:13.144][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 23:57:13.844][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:13.880][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:13.882][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:13.885][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 23:57:14.445][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:14.447][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:14.449][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:14.451][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 23:57:15.003][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:15.005][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:15.007][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:15.010][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 23:57:15.562][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:15.565][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:15.567][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:15.569][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 23:57:16.117][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:16.119][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:16.121][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:16.124][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 23:57:16.681][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:16.683][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:16.685][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:16.687][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 23:57:17.242][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:17.243][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:17.263][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:17.266][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 23:57:17.817][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:17.819][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:17.821][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:17.823][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 23:57:18.377][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:18.379][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:18.381][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:18.383][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 23:57:18.935][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:18.937][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:18.939][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:18.942][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 23:57:19.719][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:19.728][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:19.731][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:19.733][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-04-15 23:57:20.287][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:20.289][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:20.292][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:20.294][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-04-15 23:57:20.829][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:20.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:20.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:20.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:20.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:20.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:20.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:20.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:20.856][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-04-15 23:57:20.862][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:20.864][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:20.868][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-04-15 23:57:21.422][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:21.424][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:21.426][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[2024-04-15 23:57:21.428][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-04-15 23:57:22.282][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:22.284][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:22.286][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:22.289][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-04-15 23:57:22.841][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:22.867][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:22.870][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[2024-04-15 23:57:22.873][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-04-15 23:57:23.440][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:23.442][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:23.444][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:23.448][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-04-15 23:57:24.008][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:24.010][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:24.013][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[2024-04-15 23:57:24.015][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-04-15 23:57:24.565][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:24.567][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:24.569][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:24.572][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-04-15 23:57:25.124][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:25.127][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:25.130][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[2024-04-15 23:57:25.133][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-04-15 23:57:25.815][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:25.817][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:25.819][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:25.822][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-04-15 23:57:26.366][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:26.368][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:26.372][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[2024-04-15 23:57:26.374][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-04-15 23:57:27.325][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:27.351][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:27.353][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:27.356][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-04-15 23:57:27.912][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:27.914][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:27.917][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[2024-04-15 23:57:27.919][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-04-15 23:57:28.623][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:28.626][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:28.628][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:28.631][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-04-15 23:57:29.174][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:29.189][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:29.191][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[2024-04-15 23:57:29.194][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-04-15 23:57:29.986][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:29.989][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:29.995][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:29.998][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-04-15 23:57:30.545][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:30.553][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:30.556][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[2024-04-15 23:57:30.558][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-04-15 23:57:31.204][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:31.206][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:31.208][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:31.212][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-04-15 23:57:31.757][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:31.766][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:31.769][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[2024-04-15 23:57:31.771][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-04-15 23:57:32.510][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:32.512][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:32.514][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:32.517][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-04-15 23:57:33.072][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:33.087][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:33.090][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[2024-04-15 23:57:33.093][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.INFO [2024-04-15 23:57:33.940][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:33.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:33.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:33.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:33.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:33.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:33.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:33.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:33.967][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-04-15 23:57:33.974][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:33.994][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:33.998][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 23:57:34.543][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:34.545][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:34.547][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:34.549][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 23:57:35.101][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:35.103][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:35.106][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:35.108][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 23:57:35.665][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:35.712][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:35.760][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:35.765][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 23:57:36.308][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:36.310][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:36.313][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:36.316][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 23:57:36.868][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:36.870][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:36.873][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:36.876][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 23:57:37.417][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:37.420][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:37.423][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:37.426][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 23:57:37.971][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:37.973][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:37.975][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:37.978][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 23:57:38.533][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:38.535][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:38.537][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:38.541][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 23:57:39.090][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:39.092][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:39.094][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:39.096][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 23:57:39.980][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:39.985][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:39.987][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:39.990][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 23:57:40.540][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:40.542][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:40.545][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:40.547][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 23:57:41.103][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:41.105][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:41.107][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:41.110][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 23:57:41.671][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:41.673][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:41.676][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:41.678][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 23:57:42.226][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:42.228][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:42.231][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:42.234][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 23:57:42.784][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:42.786][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:42.789][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:42.791][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 23:57:43.696][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:43.699][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:43.701][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:43.704][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 23:57:44.262][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:44.264][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:44.265][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:44.268][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 23:57:45.065][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:57:45.067][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:45.069][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:45.072][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-04-15 23:57:45.623][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:57:45.625][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:57:45.627][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-04-15 23:57:45.630][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-04-15 23:57:46.410][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-04-15 23:57:46.444][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-04-15 23:57:46.459][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:46.462][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 3 content(s).
biodb.DEBUG[2024-04-15 23:57:46.464][self$createEntryFromContent] Parsing 3 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 23:57:46.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:46.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:46.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:46.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:46.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:46.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:46.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:46.498][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:46.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:46.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.508][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:46.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:46.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:46.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:46.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:46.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:46.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:46.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:46.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:46.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:46.553][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:46.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:46.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.636][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:46.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:46.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:46.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:46.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:46.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:46.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:46.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:46.674][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:46.677][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.TRACE[2024-04-15 23:57:46.682][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:46.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:46.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.719][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:46.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:57:46.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:46.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:46.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:46.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:46.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:46.894][self$createEntryFromContent] Accession numbers: NA, NA, NA.
biodb.DEBUG[2024-04-15 23:57:46.896][self$createEntryFromContent] Found 3 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-04-15 23:57:46.898][function(conn, opt)] Entries: [4]: "NULL, NULL, NULL, NULL"
biodb.INFO [2024-04-15 23:57:47.008][biodb::testThat]
biodb.INFO [2024-04-15 23:57:47.011][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-04-15 23:57:47.014][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:47.016][biodb::testThat]
biodb.INFO [2024-04-15 23:57:47.105][biodb::testThat]
biodb.INFO [2024-04-15 23:57:47.108][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-04-15 23:57:47.110][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:47.112][biodb::testThat]
biodb.INFO [2024-04-15 23:57:47.197][biodb::testThat]
biodb.INFO [2024-04-15 23:57:47.199][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-04-15 23:57:47.200][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:47.202][biodb::testThat]
biodb.DEBUG[2024-04-15 23:57:47.208][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-04-15 23:57:47.215][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:47.217][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:47.221][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-04-15 23:57:51.328][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-04-15 23:57:57.419][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:57.424][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-04-15 23:57:57.697][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-04-15 23:57:59.575][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:59.577][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:59.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.582][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.601][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.604][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.608][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 23:57:59.612][biodb::testThat]
biodb.INFO [2024-04-15 23:57:59.614][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-04-15 23:57:59.616][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:59.618][biodb::testThat]
biodb.ERROR[2024-04-15 23:57:59.797][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-04-15 23:57:59.834][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-04-15 23:57:59.863][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 23:57:59.866][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-04-15 23:57:59.869][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-04-15 23:57:59.870][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 23:57:59.872][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:59.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:59.876][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:59.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:59.880][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-15 23:57:59.905][biodb::testContext]
biodb.INFO [2024-04-15 23:57:59.908][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:57:59.910][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-04-15 23:57:59.911][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:57:59.914][biodb::testContext]
biodb.INFO [2024-04-15 23:57:59.918][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:57:59.926][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 23:57:59.934][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:57:59.938][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 23:57:59.940][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 23:57:59.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:59.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:59.951][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 23:57:59.954][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 23:57:59.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:59.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:59.963][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 23:57:59.966][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 23:57:59.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:59.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:59.976][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 23:57:59.989][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 23:57:59.992][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 23:57:59.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:59.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.002][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 23:58:00.004][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 23:58:00.007][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 23:58:00.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.012][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[2024-04-15 23:58:00.014][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 23:58:00.016][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 23:58:00.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.027][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 23:58:00.030][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 23:58:00.032][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 23:58:00.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.040][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[2024-04-15 23:58:00.043][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 23:58:00.045][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 23:58:00.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.054][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 23:58:00.056][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 23:58:00.059][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 23:58:00.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.066][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[2024-04-15 23:58:00.069][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:58:00.071][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 23:58:00.075][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 23:58:00.078][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 23:58:00.080][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 23:58:00.083][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 23:58:00.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.096][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 23:58:00.103][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 23:58:00.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.115][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 23:58:00.119][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 23:58:00.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.128][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 23:58:00.131][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 23:58:00.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.141][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 23:58:00.144][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 23:58:00.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.173][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 23:58:00.176][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 23:58:00.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.185][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:58:00.187][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 23:58:00.206][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 23:58:00.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.216][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 23:58:00.219][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 23:58:00.222][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 23:58:00.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.233][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 23:58:00.238][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:00.241][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 23:58:00.244][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.247][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:00.250][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.252][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:00.255][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:00.257][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:00.260][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:58:00.262][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:00.265][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.268][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 23:58:00.271][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:00.274][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.277][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.280][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:00.280][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:00.280][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:00.280][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:58:00.280][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:58:00.283][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:00.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:00.292][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:00.295][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:00.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:00.303][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:00.307][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:00.310][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.312][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:00.315][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:00.318][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:00.321][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.325][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 23:58:00.330][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:00.333][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:58:00.336][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.339][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:00.342][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.344][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:00.347][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:00.350][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:00.353][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:58:00.371][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:00.374][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.377][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 23:58:00.380][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:00.383][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.386][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.389][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:00.389][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:00.389][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:00.389][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:58:00.389][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:58:00.392][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:00.394][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:00.397][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:00.400][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:00.403][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:00.404][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:00.407][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:00.409][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.412][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:00.414][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:00.416][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:00.419][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.423][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 23:58:00.428][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.431][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 23:58:00.434][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.461][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:00.464][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.467][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:00.469][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:00.471][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:00.472][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:58:00.476][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:00.478][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:00.481][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 23:58:00.483][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:00.490][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.492][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.495][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.497][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:00.503][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:00.505][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:00.507][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:00.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:00.513][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:00.516][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:00.518][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.520][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:00.522][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:00.525][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:00.527][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.530][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 23:58:00.535][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.537][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:58:00.540][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.542][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:00.545][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.547][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:00.550][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:00.567][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:00.569][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:58:00.572][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:00.574][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:00.576][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 23:58:00.579][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:00.582][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.584][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:00.587][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.590][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:00.592][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:00.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:00.595][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:00.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:00.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:00.601][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:00.603][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:00.606][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:00.608][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:00.610][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:00.613][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:00.615][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.707][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[2024-04-15 23:58:00.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:00.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.800][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 23:58:00.803][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 23:58:00.806][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 23:58:00.809][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 23:58:00.813][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 23:58:00.816][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 23:58:00.819][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 23:58:00.822][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 23:58:00.826][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 23:58:00.829][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 23:58:00.832][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 23:58:00.837][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 23:58:00.841][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 23:58:00.844][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 23:58:00.848][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 23:58:00.851][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 23:58:00.854][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 23:58:00.858][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 23:58:00.861][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 23:58:00.864][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 23:58:00.871][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 23:58:00.875][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 23:58:00.877][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 23:58:00.884][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 23:58:00.888][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 23:58:00.891][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 23:58:00.894][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 23:58:00.917][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 23:58:00.920][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 23:58:00.924][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 23:58:00.927][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 23:58:00.931][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 23:58:00.934][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 23:58:00.937][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 23:58:00.941][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 23:58:00.944][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 23:58:00.947][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 23:58:00.971][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 23:58:00.974][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 23:58:00.978][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 23:58:00.982][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 23:58:00.986][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 23:58:00.989][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 23:58:00.992][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 23:58:00.996][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 23:58:00.999][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 23:58:01.002][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 23:58:01.005][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 23:58:01.007][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 23:58:01.008][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 23:58:01.010][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 23:58:01.013][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 23:58:01.017][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 23:58:01.020][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 23:58:01.024][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 23:58:01.028][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 23:58:01.032][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 23:58:01.035][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 23:58:01.037][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 23:58:01.040][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 23:58:01.043][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 23:58:01.046][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 23:58:01.050][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 23:58:01.053][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 23:58:01.057][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 23:58:01.060][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 23:58:01.063][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 23:58:01.067][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 23:58:01.070][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 23:58:01.074][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 23:58:01.077][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 23:58:01.081][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 23:58:01.088][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 23:58:01.091][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 23:58:01.093][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 23:58:01.096][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 23:58:01.101][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 23:58:01.105][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 23:58:01.108][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 23:58:01.111][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 23:58:01.115][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 23:58:01.118][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 23:58:01.122][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 23:58:01.126][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 23:58:01.129][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:58:01.132][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:01.134][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.138][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.140][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[2024-04-15 23:58:01.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.374][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[2024-04-15 23:58:01.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:01.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.446][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-04-15 23:58:01.449][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 23:58:01.453][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:01.456][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 23:58:01.458][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:01.461][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:01.463][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:01.465][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:01.467][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:01.469][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:01.472][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:58:01.476][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:01.478][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:01.480][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-04-15 23:58:01.482][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:01.491][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-04-15 23:58:01.491][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-04-15 23:58:01.491][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-04-15 23:58:01.491][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-04-15 23:58:01.491][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-04-15 23:58:01.491][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-04-15 23:58:01.491][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-04-15 23:58:01.491][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-04-15 23:58:01.491][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-04-15 23:58:01.493][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:01.495][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:01.495][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:01.497][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:01.499][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:01.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:01.503][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:01.507][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:01.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:01.510][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:01.512][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 23:58:01.512][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-04-15 23:58:01.516][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:01.518][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:01.520][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:01.522][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:01.525][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-04-15 23:58:01.528][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 23:58:01.535][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 23:58:01.537][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-04-15 23:58:01.540][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 23:58:01.543][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-04-15 23:58:01.546][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 23:58:01.548][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 23:58:01.552][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-04-15 23:58:01.570][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-04-15 23:58:01.573][biodb::testThat]
biodb.INFO [2024-04-15 23:58:01.576][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-04-15 23:58:01.578][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:01.580][biodb::testThat]
biodb.DEBUG[2024-04-15 23:58:01.587][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-04-15 23:58:01.616][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:01.618][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:01.622][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-04-15 23:58:02.228][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-04-15 23:58:02.840][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:02.843][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-04-15 23:58:02.853][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-04-15 23:58:02.980][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-04-15 23:58:02.989][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:02.991][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:02.995][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-04-15 23:58:03.617][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-04-15 23:58:04.239][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:04.246][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-04-15 23:58:04.258][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-04-15 23:58:04.282][biodb::testThat]
biodb.INFO [2024-04-15 23:58:04.284][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-04-15 23:58:04.286][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:04.288][biodb::testThat]
biodb.INFO [2024-04-15 23:58:04.425][biodb::testThat]
biodb.INFO [2024-04-15 23:58:04.427][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-04-15 23:58:04.433][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:04.436][biodb::testThat]
biodb.DEBUG[2024-04-15 23:58:04.442][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-04-15 23:58:04.449][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:04.451][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:04.455][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-04-15 23:58:04.905][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-04-15 23:58:05.357][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:05.361][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-04-15 23:58:05.372][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-04-15 23:58:05.384][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-04-15 23:58:05.390][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:58:05.393][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-04-15 23:58:05.397][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:58:05.400][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-04-15 23:58:05.413][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-04-15 23:58:05.458][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:05.460][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:05.465][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-04-15 23:58:05.925][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-04-15 23:58:06.374][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:06.378][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-04-15 23:58:06.387][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-04-15 23:58:06.404][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-04-15 23:58:06.416][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:06.420][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-04-15 23:58:06.423][rule$waitAsNeeded] Wait 0.0407748 second(s).
biodb.TRACE[2024-04-15 23:58:06.605][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-04-15 23:58:07.803][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-04-15 23:58:09.300][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:09.305][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-04-15 23:58:09.401][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-04-15 23:58:09.666][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-04-15 23:58:09.676][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:09.678][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:09.689][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-04-15 23:58:10.947][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-04-15 23:58:12.459][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:12.508][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-04-15 23:58:12.556][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-04-15 23:58:12.831][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 23:58:12.834][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-04-15 23:58:12.836][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-04-15 23:58:12.839][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 23:58:12.841][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:12.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:12.844][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:12.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:12.849][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:12.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-15 23:58:12.860][biodb::testContext]
biodb.INFO [2024-04-15 23:58:12.864][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:58:12.867][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-04-15 23:58:12.869][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:58:12.871][biodb::testContext]
biodb.INFO [2024-04-15 23:58:12.875][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:58:12.879][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 23:58:12.888][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:12.890][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 23:58:12.916][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 23:58:12.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:12.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:12.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:12.977][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 23:58:12.980][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 23:58:12.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:12.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:12.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:12.995][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 23:58:12.997][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 23:58:12.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.009][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 23:58:13.012][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 23:58:13.024][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 23:58:13.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.039][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.DEBUG[2024-04-15 23:58:13.041][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 23:58:13.043][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 23:58:13.048][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 23:58:13.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.056][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 23:58:13.059][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 23:58:13.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.066][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[2024-04-15 23:58:13.068][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 23:58:13.070][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 23:58:13.072][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 23:58:13.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.080][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 23:58:13.083][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 23:58:13.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.088][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[2024-04-15 23:58:13.090][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 23:58:13.093][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 23:58:13.095][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 23:58:13.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.104][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:58:13.106][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 23:58:13.108][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 23:58:13.111][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 23:58:13.113][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 23:58:13.115][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 23:58:13.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.121][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[2024-04-15 23:58:13.123][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 23:58:13.126][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 23:58:13.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.135][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 23:58:13.137][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 23:58:13.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.212][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 23:58:13.214][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 23:58:13.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.223][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 23:58:13.226][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 23:58:13.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.234][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 23:58:13.237][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 23:58:13.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.246][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:58:13.248][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 23:58:13.275][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 23:58:13.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.283][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 23:58:13.286][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 23:58:13.288][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 23:58:13.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.297][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 23:58:13.302][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.304][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 23:58:13.307][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.310][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:13.312][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.314][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.317][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.319][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.321][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:58:13.324][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:13.326][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.328][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 23:58:13.330][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:13.333][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.335][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.338][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:13.338][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:13.338][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:13.338][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:58:13.338][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:58:13.340][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:13.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.347][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:13.349][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.351][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.353][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.355][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.370][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:13.412][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:13.414][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.416][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.419][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 23:58:13.423][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.426][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:58:13.429][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.431][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:13.434][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.436][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.439][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.441][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.444][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:58:13.446][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:13.448][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.450][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 23:58:13.452][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:13.455][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.457][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.461][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:13.461][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:13.461][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:13.461][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:58:13.461][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:58:13.468][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:13.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.474][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:13.481][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.483][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.486][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.489][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.492][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:13.494][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:13.497][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.499][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.502][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 23:58:13.506][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.509][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 23:58:13.511][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.513][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:13.516][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.518][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.520][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.522][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.525][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:58:13.529][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:13.531][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.534][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 23:58:13.536][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:13.538][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.541][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.543][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.545][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:13.558][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.561][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.564][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:13.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.569][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.571][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.574][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.576][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:13.579][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:13.581][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.584][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.586][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 23:58:13.590][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.593][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:58:13.595][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.599][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:13.602][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.604][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.606][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.609][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.611][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:58:13.613][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:13.615][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.617][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 23:58:13.619][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:13.621][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.624][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.659][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.677][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:13.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.686][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:13.688][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.696][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.698][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.701][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.703][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:13.705][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:13.738][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.771][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.775][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:13.777][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.888][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[2024-04-15 23:58:13.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.976][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 23:58:13.979][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 23:58:13.982][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 23:58:13.985][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 23:58:13.988][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 23:58:13.991][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 23:58:13.995][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 23:58:13.998][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 23:58:14.001][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 23:58:14.004][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 23:58:14.007][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 23:58:14.010][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 23:58:14.013][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 23:58:14.016][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 23:58:14.019][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 23:58:14.023][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 23:58:14.027][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 23:58:14.030][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 23:58:14.035][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 23:58:14.038][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 23:58:14.042][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 23:58:14.046][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 23:58:14.049][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 23:58:14.056][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 23:58:14.060][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 23:58:14.066][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 23:58:14.069][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 23:58:14.073][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 23:58:14.076][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 23:58:14.080][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 23:58:14.084][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 23:58:14.087][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 23:58:14.090][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 23:58:14.094][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 23:58:14.097][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 23:58:14.100][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 23:58:14.103][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 23:58:14.106][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 23:58:14.108][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 23:58:14.112][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 23:58:14.114][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 23:58:14.116][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 23:58:14.119][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 23:58:14.122][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 23:58:14.126][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 23:58:14.129][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 23:58:14.132][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 23:58:14.135][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 23:58:14.139][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 23:58:14.142][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 23:58:14.145][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 23:58:14.159][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 23:58:14.161][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 23:58:14.163][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 23:58:14.165][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 23:58:14.169][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 23:58:14.172][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 23:58:14.176][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 23:58:14.179][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 23:58:14.182][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 23:58:14.185][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 23:58:14.188][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 23:58:14.191][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 23:58:14.194][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 23:58:14.197][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 23:58:14.199][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 23:58:14.201][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 23:58:14.205][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 23:58:14.208][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 23:58:14.211][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 23:58:14.215][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 23:58:14.218][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 23:58:14.222][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 23:58:14.225][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 23:58:14.229][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 23:58:14.233][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 23:58:14.237][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 23:58:14.241][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 23:58:14.244][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 23:58:14.254][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 23:58:14.257][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 23:58:14.261][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 23:58:14.267][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 23:58:14.271][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 23:58:14.276][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:58:14.279][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:14.281][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.285][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.372][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[2024-04-15 23:58:14.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.616][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-04-15 23:58:14.619][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 23:58:14.624][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:14.626][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 23:58:14.628][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:14.631][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:14.633][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:14.635][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:14.638][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:14.640][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:14.643][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:58:14.645][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:14.648][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:14.650][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-04-15 23:58:14.653][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:14.655][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-04-15 23:58:14.655][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-04-15 23:58:14.655][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-04-15 23:58:14.655][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-04-15 23:58:14.655][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-04-15 23:58:14.655][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-04-15 23:58:14.655][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-04-15 23:58:14.655][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-04-15 23:58:14.655][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-04-15 23:58:14.658][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:14.661][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:14.661][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:14.663][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:14.666][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:14.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:14.672][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:14.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:14.676][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:14.677][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:14.690][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 23:58:14.690][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-04-15 23:58:14.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:14.693][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:14.694][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:14.696][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:14.697][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-04-15 23:58:14.700][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 23:58:14.707][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 23:58:14.709][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-04-15 23:58:14.713][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 23:58:14.716][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-04-15 23:58:14.719][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 23:58:14.721][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 23:58:14.724][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-04-15 23:58:14.727][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-04-15 23:58:14.730][biodb::testThat]
biodb.INFO [2024-04-15 23:58:14.732][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-04-15 23:58:14.734][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:14.736][biodb::testThat]
biodb.DEBUG[2024-04-15 23:58:14.744][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-04-15 23:58:14.752][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:58:14.755][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-04-15 23:58:14.758][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:58:14.820][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-04-15 23:58:16.847][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-04-15 23:58:16.849][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-04-15 23:58:16.853][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-04-15 23:58:16.856][cch$loadFileContent] file.exist = [2]: "FALSE, TRUE".
biodb.TRACE[2024-04-15 23:58:16.858][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-04-15 23:58:16.861][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:58:16.864][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 23:58:16.866][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:58:16.868][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:58:16.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:16.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:16.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:16.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:16.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:16.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.948][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-04-15 23:58:16.954][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:16.957][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:16.959][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-04-15 23:58:17.518][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:58:17.520][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:58:17.521][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[2024-04-15 23:58:17.523][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-04-15 23:58:18.337][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:58:18.345][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:18.347][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:18.350][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-04-15 23:58:18.900][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:58:18.915][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:58:18.917][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[2024-04-15 23:58:18.920][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-04-15 23:58:19.666][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:58:19.670][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:19.672][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:19.675][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-04-15 23:58:20.237][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:58:20.239][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:58:20.241][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[2024-04-15 23:58:20.243][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-04-15 23:58:20.872][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:58:20.875][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:20.878][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:20.880][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-04-15 23:58:21.514][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:58:21.522][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:58:21.524][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[2024-04-15 23:58:21.526][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-04-15 23:58:22.464][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:58:22.466][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:22.467][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:22.469][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-04-15 23:58:23.142][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:58:23.144][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:58:23.145][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[2024-04-15 23:58:23.148][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-04-15 23:58:23.980][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:58:23.983][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:23.986][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:23.989][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-04-15 23:58:24.615][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:58:24.620][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:58:24.622][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[2024-04-15 23:58:24.625][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-04-15 23:58:25.179][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:58:25.181][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:25.182][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:25.185][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-04-15 23:58:25.735][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:58:25.738][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:58:25.740][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[2024-04-15 23:58:25.742][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-04-15 23:58:26.711][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:58:26.713][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:26.715][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:26.718][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-04-15 23:58:27.269][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:58:27.274][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:58:27.277][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[2024-04-15 23:58:27.279][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-04-15 23:58:28.071][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:58:28.073][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:28.076][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:28.078][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-04-15 23:58:28.629][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:58:28.631][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:58:28.634][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[2024-04-15 23:58:28.636][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-04-15 23:58:29.398][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-04-15 23:58:29.401][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:29.403][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:29.406][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-04-15 23:58:29.952][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-04-15 23:58:29.956][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-04-15 23:58:29.958][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[2024-04-15 23:58:29.961][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-04-15 23:58:30.992][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.TRACE[2024-04-15 23:58:30.997][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2024-04-15 23:58:31.002][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:58:31.005][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-04-15 23:58:31.007][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 23:58:31.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:31.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:31.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:31.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:31.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:31.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:31.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:58:31.037][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:58:31.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:58:31.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.047][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:58:31.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:58:31.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:31.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:31.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:58:31.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:31.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:31.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:31.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:31.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:31.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:31.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:58:31.122][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:58:31.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:58:31.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.132][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:58:31.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 23:58:31.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:31.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:31.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:31.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:31.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:31.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:31.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:31.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:31.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:31.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:31.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:31.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:31.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:31.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:31.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:31.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:31.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:31.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:31.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:31.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:31.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:31.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:31.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:31.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:31.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:58:31.260][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-04-15 23:58:31.262][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-04-15 23:58:31.268][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-15 23:58:31.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:31.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:31.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:31.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:31.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:31.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:31.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:58:31.312][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-04-15 23:58:31.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:31.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:31.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:31.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:31.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:31.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:31.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:58:31.337][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-04-15 23:58:31.340][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-04-15 23:58:31.342][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-04-15 23:58:31.357][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 23:58:31.360][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-04-15 23:58:31.361][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-04-15 23:58:31.363][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 23:58:31.364][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:31.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:31.371][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:31.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:31.375][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:31.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 101 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_100_generic.R:16:1'): RT unit is defined when there is an RT value. ──
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_100_generic.R:16:1'): We can search for an entry by searchable field ──
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_100_generic.R:16:1'): We can search for an entry by searchable field ──
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
── Failure ('test_100_generic.R:16:1'): We can search for an entry by name. ────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_100_generic.R:16:1'): We can search for an entry by name. ──────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
── Failure ('test_100_generic.R:16:1'): We can load an entry from the database. ──
any(vapply(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.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_100_generic.R:16:1'): We can load an entry from the database. ──
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(db = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_100_generic.R:16:1'): We can search for a compound ─────────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(db = `<LpdmpsSC>`, opt = `<named list>`)
── Error ('test_100_generic.R:16:1'): annotateMzValues() accepts a single vector. ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_100_generic.R:16:1'): ppm tolerance works in annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_100_generic.R:16:1'): Input data frame is not modified by annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── 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 14 | WARN 0 | SKIP 0 | PASS 101 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn3.7441.1465.340
LipidmapsStructureEntry0.7050.0210.738