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This page was generated on 2024-05-07 11:32:30 -0400 (Tue, 07 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4461
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Package 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for biodbLipidmaps on kjohnson3


To the developers/maintainers of the biodbLipidmaps package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: biodbLipidmaps
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-05-06 19:59:10 -0400 (Mon, 06 May 2024)
EndedAt: 2024-05-06 19:59:38 -0400 (Mon, 06 May 2024)
EllapsedTime: 28.3 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
  any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  One of the entries is NULL.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
   3.   └─testthat::expect_false(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 161 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/biodbLipidmaps.Rcheck/00check.log’
for details.

Installation output

biodbLipidmaps.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbLipidmaps' is deprecated and will be removed from
  Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-05-06 19:59:29.238][biodb::testContext]
biodb.INFO [2024-05-06 19:59:29.239][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:29.240][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-06 19:59:29.240][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:29.240][biodb::testContext]
biodb.INFO [2024-05-06 19:59:29.243][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:29.244][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:29.247][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:29.247][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-06 19:59:29.247][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-06 19:59:29.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.249][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-06 19:59:29.255][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-06 19:59:29.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.261][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-06 19:59:29.261][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-06 19:59:29.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.262][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-06 19:59:29.262][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-06 19:59:29.262][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-06 19:59:29.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.263][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-06 19:59:29.263][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-06 19:59:29.264][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-06 19:59:29.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.264][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-06 19:59:29.265][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-06 19:59:29.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.266][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-06 19:59:29.266][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-06 19:59:29.266][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-06 19:59:29.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.267][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-06 19:59:29.267][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-06 19:59:29.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.268][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-06 19:59:29.268][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-06 19:59:29.268][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-06 19:59:29.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.269][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:29.270][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-06 19:59:29.270][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-06 19:59:29.270][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-06 19:59:29.270][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-06 19:59:29.271][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-06 19:59:29.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.271][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-06 19:59:29.272][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-06 19:59:29.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.272][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-06 19:59:29.273][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-06 19:59:29.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.274][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-06 19:59:29.274][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-06 19:59:29.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.275][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-06 19:59:29.275][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-06 19:59:29.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.276][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-06 19:59:29.276][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-06 19:59:29.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.277][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:29.277][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-06 19:59:29.283][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-06 19:59:29.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.284][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-06 19:59:29.285][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-06 19:59:29.285][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-06 19:59:29.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.287][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-06 19:59:29.298][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.302][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-06 19:59:29.302][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.303][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:29.303][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.303][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.303][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.304][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.304][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:29.304][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:29.304][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.305][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-06 19:59:29.305][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:29.305][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.305][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.306][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:29.306][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:29.306][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:29.306][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:29.306][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:29.306][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:29.306][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:29.306][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:29.307][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:29.307][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:29.307][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:29.307][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.307][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.308][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:29.308][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:29.308][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.308][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.309][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-06 19:59:29.309][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.309][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:29.310][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.310][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:29.310][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.310][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.311][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.311][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.311][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:29.311][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:29.311][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.312][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-06 19:59:29.312][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:29.312][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.312][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.313][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:29.313][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:29.313][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:29.313][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:29.313][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:29.313][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:29.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:29.313][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:29.314][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:29.314][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:29.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:29.314][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.315][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.317][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:29.317][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:29.317][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.318][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.318][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-06 19:59:29.318][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.319][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-06 19:59:29.319][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.319][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:29.319][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.320][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.320][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.320][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.320][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:29.320][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:29.321][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.321][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-06 19:59:29.321][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:29.321][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.322][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.322][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.322][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:29.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:29.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:29.323][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:29.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:29.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:29.323][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.324][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.324][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:29.324][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:29.324][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.325][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.325][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-06 19:59:29.325][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.326][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:29.326][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.326][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:29.326][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.326][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.327][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.327][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.327][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:29.327][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:29.328][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.328][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-06 19:59:29.328][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:29.328][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.329][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.329][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.329][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:29.329][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:29.329][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:29.330][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:29.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:29.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:29.330][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.331][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.331][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:29.331][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:29.331][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.331][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.333][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:29.333][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.336][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[2024-05-06 19:59:29.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.337][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[2024-05-06 19:59:29.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.340][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[2024-05-06 19:59:29.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.349][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[2024-05-06 19:59:29.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.351][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-06 19:59:29.353][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-06 19:59:29.354][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-06 19:59:29.354][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-06 19:59:29.355][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-06 19:59:29.355][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-06 19:59:29.356][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:29.356][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:29.356][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-06 19:59:29.357][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-06 19:59:29.357][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-06 19:59:29.357][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-06 19:59:29.358][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:29.358][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:29.359][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-06 19:59:29.359][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-06 19:59:29.359][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-06 19:59:29.360][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-06 19:59:29.360][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-06 19:59:29.360][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-06 19:59:29.361][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-06 19:59:29.361][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-06 19:59:29.362][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-06 19:59:29.362][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-06 19:59:29.362][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-06 19:59:29.363][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-06 19:59:29.363][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-06 19:59:29.363][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-06 19:59:29.364][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-06 19:59:29.364][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-06 19:59:29.365][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-06 19:59:29.367][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-06 19:59:29.368][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-06 19:59:29.368][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-06 19:59:29.368][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-06 19:59:29.369][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-06 19:59:29.369][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-06 19:59:29.369][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-06 19:59:29.370][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-06 19:59:29.370][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-06 19:59:29.371][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-06 19:59:29.371][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-06 19:59:29.371][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-06 19:59:29.372][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-06 19:59:29.372][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-06 19:59:29.372][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-06 19:59:29.373][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-06 19:59:29.373][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-06 19:59:29.373][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-06 19:59:29.374][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-06 19:59:29.374][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-06 19:59:29.374][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-06 19:59:29.375][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-06 19:59:29.375][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-06 19:59:29.376][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-06 19:59:29.376][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-06 19:59:29.376][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-06 19:59:29.377][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-06 19:59:29.377][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-06 19:59:29.377][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-06 19:59:29.378][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-06 19:59:29.378][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-06 19:59:29.379][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-06 19:59:29.379][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-06 19:59:29.379][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-06 19:59:29.380][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-06 19:59:29.380][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-06 19:59:29.380][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-06 19:59:29.381][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-06 19:59:29.381][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-06 19:59:29.381][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-06 19:59:29.382][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-06 19:59:29.382][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-06 19:59:29.383][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-06 19:59:29.383][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-06 19:59:29.383][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-06 19:59:29.384][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-06 19:59:29.384][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-06 19:59:29.384][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-06 19:59:29.385][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-06 19:59:29.385][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-06 19:59:29.385][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-06 19:59:29.386][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-06 19:59:29.388][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-06 19:59:29.388][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:29.390][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:29.390][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.390][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.400][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[2024-05-06 19:59:29.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.411][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[2024-05-06 19:59:29.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.414][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[2024-05-06 19:59:29.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.419][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[2024-05-06 19:59:29.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:29.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:29.421][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:29.424][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-06 19:59:29.425][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.425][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.425][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.426][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:29.426][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.426][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.426][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.427][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.427][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:29.427][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:29.427][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.428][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-06 19:59:29.428][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:29.428][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-06 19:59:29.428][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-06 19:59:29.428][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-06 19:59:29.428][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-06 19:59:29.428][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-06 19:59:29.428][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-06 19:59:29.428][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-06 19:59:29.428][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-06 19:59:29.428][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-06 19:59:29.429][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:29.429][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:29.429][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:29.429][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:29.429][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:29.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:29.430][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:29.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:29.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:29.430][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:29.431][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-06 19:59:29.431][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-06 19:59:29.431][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:29.431][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:29.431][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:29.432][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:29.433][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-06 19:59:29.434][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-06 19:59:29.445][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-06 19:59:29.445][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-06 19:59:29.447][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-06 19:59:29.448][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-06 19:59:29.450][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-06 19:59:29.451][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-06 19:59:29.451][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-06 19:59:29.451][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-06 19:59:29.455][biodb::testThat]
biodb.INFO [2024-05-06 19:59:29.456][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-06 19:59:29.456][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:29.456][biodb::testThat]
biodb.TRACE[2024-05-06 19:59:29.457][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-05-06 19:59:29.458][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-06 19:59:29.459][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-06 19:59:29.463][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:29.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.469][FUN] Functions in observer BiodbConfig: [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[2024-05-06 19:59:29.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:29.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:29.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.481][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-06 19:59:29.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-06 19:59:29.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.482][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:29.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:29.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.483][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.496][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.497][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.499][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-06 19:59:29.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.500][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-06 19:59:29.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.501][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:29.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:29.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.502][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:29.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:29.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.505][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.506][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-06 19:59:29.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.507][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-06 19:59:29.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.510][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-06 19:59:29.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.516][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.528][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.546][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.547][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.549][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:29.556][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-06 19:59:29.557][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-06 19:59:29.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-06 19:59:29.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.558][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-06 19:59:29.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-06 19:59:29.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.559][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-06 19:59:29.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-06 19:59:29.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-06 19:59:29.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-06 19:59:29.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.574][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.584][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.585][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.586][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.596][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.596][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.596][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.600][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.603][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.604][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.604][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.604][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.608][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.609][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.610][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.611][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.612][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.612][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.612][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.616][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:29.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:29.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.617][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:29.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:29.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.618][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:29.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:29.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.619][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:29.619][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:29.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.619][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.620][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:29.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:29.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.626][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.626][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.627][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.631][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.632][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.633][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.634][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.635][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.635][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.635][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.641][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.642][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.642][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.644][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.644][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.645][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.646][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:29.647][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:29.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.647][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.649][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.649][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.649][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.649][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.651][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.651][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.652][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.653][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.654][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.654][ef$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:29.657][biodb::testThat]
biodb.INFO [2024-05-06 19:59:29.658][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-06 19:59:29.658][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:29.658][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:29.663][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-05-06 19:59:29.666][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-06 19:59:29.667][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-05-06 19:59:29.668][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:29.668][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-05-06 19:59:29.669][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-06 19:59:29.676][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-06 19:59:29.676][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-06 19:59:29.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:29.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:29.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:29.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:29.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:29.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:29.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:29.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:29.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:29.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:29.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:29.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.685][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-06 19:59:29.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-06 19:59:29.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.686][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:29.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:29.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.687][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.691][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:29.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.692][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.693][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:29.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.694][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-06 19:59:29.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.695][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-06 19:59:29.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.696][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:29.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:29.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.697][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:29.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:29.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.700][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-06 19:59:29.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.701][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-06 19:59:29.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.705][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-06 19:59:29.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.710][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.711][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.712][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.714][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:29.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:29.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:29.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:29.721][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-05-06 19:59:29.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-06 19:59:29.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-06 19:59:29.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-06 19:59:29.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-06 19:59:29.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-06 19:59:29.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-06 19:59:29.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:29.727][biodb::testThat]
biodb.INFO [2024-05-06 19:59:29.727][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-06 19:59:29.727][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:29.728][biodb::testThat]
biodb.TRACE[2024-05-06 19:59:29.729][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.729][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.729][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:29.732][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-05-06 19:59:29.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:29.745][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-06 19:59:29.747][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-06 19:59:29.754][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:29.759][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-06 19:59:29.759][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:29.760][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-05-06 19:59:29.761][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-05-06 19:59:29.765][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.766][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:29.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.766][ef$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:29.768][biodb::testThat]
biodb.INFO [2024-05-06 19:59:29.768][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-06 19:59:29.768][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:29.768][biodb::testThat]
biodb.TRACE[2024-05-06 19:59:29.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:29.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:29.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:29.816][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-06 19:59:29.817][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:29.818][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-06 19:59:29.818][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:29.819][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-05-06 19:59:29.827][biodb::testThat]
biodb.INFO [2024-05-06 19:59:29.827][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-06 19:59:29.827][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:29.827][biodb::testThat]
biodb.TRACE[2024-05-06 19:59:29.834][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-06 19:59:29.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-06 19:59:29.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.835][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-06 19:59:29.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-06 19:59:29.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.836][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-06 19:59:29.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-06 19:59:29.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.837][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-06 19:59:29.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-06 19:59:29.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.851][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-06 19:59:29.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-06 19:59:29.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.852][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-06 19:59:29.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-06 19:59:29.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.853][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-06 19:59:29.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-06 19:59:29.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:29.854][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-06 19:59:29.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-06 19:59:29.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:29.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:29.858][biodb::testThat]
biodb.INFO [2024-05-06 19:59:29.858][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-06 19:59:29.858][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:29.858][biodb::testThat]
biodb.INFO [2024-05-06 19:59:29.861][biodb::testThat]
biodb.INFO [2024-05-06 19:59:29.861][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-06 19:59:29.862][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:29.862][biodb::testThat]
biodb.INFO [2024-05-06 19:59:29.867][biodb::testThat]
biodb.INFO [2024-05-06 19:59:29.867][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-06 19:59:29.867][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:29.868][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:29.869][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-05-06 19:59:31.271][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-05-06 19:59:31.680][biodb::testThat]
biodb.INFO [2024-05-06 19:59:31.680][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-06 19:59:31.680][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:31.681][biodb::testThat]
biodb.TRACE[2024-05-06 19:59:31.683][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:31.683][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:31.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:31.683][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:31.684][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:31.684][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:31.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:31.689][ef$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:31.690][biodb::testThat]
biodb.INFO [2024-05-06 19:59:31.690][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-06 19:59:31.690][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:31.691][biodb::testThat]
biodb.TRACE[2024-05-06 19:59:31.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:31.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:31.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:31.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:31.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:31.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:31.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:31.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:31.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:31.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:31.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:31.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:31.721][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-06 19:59:31.723][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:31.723][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-06 19:59:31.723][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:31.724][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-05-06 19:59:31.744][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-05-06 19:59:31.745][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:31.746][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-05-06 19:59:31.746][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:31.746][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-05-06 19:59:31.751][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-06 19:59:31.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-06 19:59:31.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:31.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:31.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:31.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:31.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:31.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:31.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:31.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:31.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:31.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:31.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:31.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:31.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:31.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:31.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:31.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:31.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:31.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:31.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:31.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:31.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:31.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:31.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:31.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:31.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:31.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:31.765][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-06 19:59:31.766][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:31.767][cch$loadFileContent] Trying to load 1 files from cache: [1]: "304383a7dc8c451be84009e31d831359".
biodb.TRACE[2024-05-06 19:59:31.768][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:31.791][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content".
biodb.DEBUG[2024-05-06 19:59:32.281][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-05-06 19:59:32.282][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:32.282][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7f71825f1888a7b29e4b8407502d21e3".
biodb.TRACE[2024-05-06 19:59:32.283][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:32.283][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content".
biodb.DEBUG[2024-05-06 19:59:32.290][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-05-06 19:59:32.291][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:32.291][cch$loadFileContent] Trying to load 1 files from cache: [1]: "fd41c675dd237f33cdaafcbb15058c54".
biodb.TRACE[2024-05-06 19:59:32.291][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:32.292][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content".
biodb.TRACE[2024-05-06 19:59:32.297][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-06 19:59:32.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-06 19:59:32.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:32.301][biodb::testThat]
biodb.INFO [2024-05-06 19:59:32.301][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-06 19:59:32.301][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:32.302][biodb::testThat]
biodb.TRACE[2024-05-06 19:59:32.302][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-06 19:59:32.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-06 19:59:32.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:32.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:32.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:32.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:32.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:32.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:32.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:32.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:32.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:32.312][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[2024-05-06 19:59:32.313][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-06 19:59:32.314][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:32.315][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-05-06 19:59:32.315][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:32.336][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-05-06 19:59:32.697][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-05-06 19:59:32.710][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-06 19:59:32.710][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-05-06 19:59:32.711][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-06 19:59:32.712][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv".
biodb.DEBUG[2024-05-06 19:59:32.712][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-06 19:59:32.713][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-06 19:59:32.713][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-06 19:59:32.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:32.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:32.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:32.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:32.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:32.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:32.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:32.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:32.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:32.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:32.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:32.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.721][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-06 19:59:32.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-06 19:59:32.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.722][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:32.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:32.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.723][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:32.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:32.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.724][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:32.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:32.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.725][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:32.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:32.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.726][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:32.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:32.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.727][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-06 19:59:32.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.728][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-06 19:59:32.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:32.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:32.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.730][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:32.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:32.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:32.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:32.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.733][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-06 19:59:32.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.734][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-06 19:59:32.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:32.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.736][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:32.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.737][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-06 19:59:32.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.738][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.739][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.741][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:32.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:32.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:32.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:32.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:32.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:32.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:32.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:32.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:32.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:32.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.752][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-06 19:59:32.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-06 19:59:32.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.753][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:32.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:32.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.754][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:32.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:32.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.755][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:32.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:32.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.756][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:32.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:32.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.757][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:32.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:32.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.758][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-06 19:59:32.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.759][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-06 19:59:32.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.760][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:32.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:32.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.761][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:32.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:32.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:32.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:32.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.764][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-06 19:59:32.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.765][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-06 19:59:32.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:32.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:32.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.768][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-06 19:59:32.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:32.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.769][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.770][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.778][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:32.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:32.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:32.786][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-05-06 19:59:32.789][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-06 19:59:32.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:32.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:32.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:32.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:32.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:32.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:32.792][FUN] Functions in observer BiodbConfig: [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[2024-05-06 19:59:32.792][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.793][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.794][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:32.794][private$selectFields]
biodb.TRACE[2024-05-06 19:59:32.795][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-06 19:59:32.795][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-06 19:59:32.795][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:32.795][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.795][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.796][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.796][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.796][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.797][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.797][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:32.797][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:32.797][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.798][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.798][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.798][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-06 19:59:32.798][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.799][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.800][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.804][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-06 19:59:32.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:32.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:32.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:32.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:32.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:32.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:32.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:32.807][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.808][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.809][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:32.809][private$selectFields]
biodb.TRACE[2024-05-06 19:59:32.809][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-06 19:59:32.809][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-06 19:59:32.809][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:32.810][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.810][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.810][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.811][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.811][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.811][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.811][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:32.812][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:32.812][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.812][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.812][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.813][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-06 19:59:32.813][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.814][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.815][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.816][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-06 19:59:32.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:32.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:32.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:32.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:32.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:32.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:32.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:32.818][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.819][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.820][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:32.820][private$selectFields]
biodb.TRACE[2024-05-06 19:59:32.821][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-06 19:59:32.821][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-06 19:59:32.821][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:32.821][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.822][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.822][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.822][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.822][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.823][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.823][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:32.823][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:32.823][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.824][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.824][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.824][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-06 19:59:32.825][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.825][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.826][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:32.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.827][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-06 19:59:32.827][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-06 19:59:32.828][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-06 19:59:32.830][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-06 19:59:32.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-06 19:59:32.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:32.832][biodb::testThat]
biodb.INFO [2024-05-06 19:59:32.833][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-06 19:59:32.833][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:32.833][biodb::testThat]
biodb.TRACE[2024-05-06 19:59:32.834][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-06 19:59:32.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-06 19:59:32.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:32.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:32.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:32.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:32.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:32.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:32.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:32.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:32.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:32.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:32.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:32.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:32.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:32.862][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-05-06 19:59:32.863][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:32.864][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5652f5994fce967a05a065a71bac3ed6".
biodb.TRACE[2024-05-06 19:59:32.865][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:32.886][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content".
biodb.DEBUG[2024-05-06 19:59:33.272][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-06 19:59:33.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:33.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:33.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:33.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:33.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:33.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:33.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:33.286][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.287][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.294][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.295][private$selectFields]
biodb.TRACE[2024-05-06 19:59:33.295][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-06 19:59:33.295][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-06 19:59:33.296][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.296][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.296][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.297][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.297][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.297][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.298][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.298][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.301][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.301][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.302][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.302][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.303][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-06 19:59:33.303][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.304][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.305][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.307][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-06 19:59:33.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:33.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:33.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:33.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:33.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:33.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:33.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:33.311][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.312][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.313][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.313][private$selectFields]
biodb.TRACE[2024-05-06 19:59:33.314][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-06 19:59:33.314][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-06 19:59:33.314][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.314][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.315][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.315][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.315][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.316][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.316][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.317][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.317][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.317][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.317][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.318][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.318][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-06 19:59:33.319][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.320][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.321][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.322][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-06 19:59:33.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:33.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:33.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:33.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:33.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:33.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:33.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:33.326][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.327][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.328][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.328][private$selectFields]
biodb.TRACE[2024-05-06 19:59:33.329][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-06 19:59:33.329][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-06 19:59:33.329][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.329][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.330][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.330][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.331][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.331][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.331][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.332][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.332][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.332][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.333][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.333][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.333][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-06 19:59:33.334][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.335][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.336][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.337][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-06 19:59:33.338][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-06 19:59:33.338][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-06 19:59:33.341][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-06 19:59:33.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-06 19:59:33.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:33.344][biodb::testThat]
biodb.INFO [2024-05-06 19:59:33.344][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-06 19:59:33.344][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:33.345][biodb::testThat]
biodb.TRACE[2024-05-06 19:59:33.346][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-06 19:59:33.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-06 19:59:33.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:33.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-06 19:59:33.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:33.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:33.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:33.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:33.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:33.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:33.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:33.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:33.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:33.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:33.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:33.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:33.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:33.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:33.363][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:33.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:33.364][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-05-06 19:59:33.365][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:33.365][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-05-06 19:59:33.366][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:33.385][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-05-06 19:59:33.867][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-06 19:59:33.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:33.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:33.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:33.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:33.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:33.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:33.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:33.872][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.873][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.874][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.874][private$selectFields]
biodb.TRACE[2024-05-06 19:59:33.874][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-06 19:59:33.874][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-06 19:59:33.875][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.875][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.875][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.876][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.876][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.876][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.877][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.877][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.877][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.877][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.878][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.878][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.878][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-06 19:59:33.879][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.880][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.881][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.882][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-05-06 19:59:33.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:33.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:33.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:33.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:33.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:33.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:33.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:33.885][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.886][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.887][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.887][private$selectFields]
biodb.TRACE[2024-05-06 19:59:33.888][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-06 19:59:33.888][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-06 19:59:33.888][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.888][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.889][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.889][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.889][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.890][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.890][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.890][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.891][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.891][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.891][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.892][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.892][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-06 19:59:33.892][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.893][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.894][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.895][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-05-06 19:59:33.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:33.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:33.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:33.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:33.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:33.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:33.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:33.898][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.899][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.900][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.901][private$selectFields]
biodb.TRACE[2024-05-06 19:59:33.901][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-06 19:59:33.901][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-06 19:59:33.901][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.902][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.902][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.902][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.903][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.903][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.903][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.903][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.904][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:33.904][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.904][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.905][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.905][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-05-06 19:59:33.905][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.906][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.907][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.908][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-05-06 19:59:33.908][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-06 19:59:33.909][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-06 19:59:33.915][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-06 19:59:33.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-06 19:59:33.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:33.917][biodb::testThat]
biodb.INFO [2024-05-06 19:59:33.917][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-06 19:59:33.917][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:33.918][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:33.918][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-06 19:59:33.919][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-06 19:59:33.919][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-06 19:59:33.919][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:33.920][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv".
biodb.DEBUG[2024-05-06 19:59:33.921][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-06 19:59:33.921][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-05-06 19:59:33.921][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-06 19:59:33.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:33.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:33.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:33.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:33.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:33.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:33.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:33.926][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.927][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:33.934][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-05-06 19:59:33.934][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-06 19:59:33.937][biodb::testThat]
biodb.INFO [2024-05-06 19:59:33.937][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-06 19:59:33.938][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:33.938][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:33.940][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-05-06 19:59:33.940][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-05-06 19:59:33.941][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-06 19:59:33.941][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-05-06 19:59:33.941][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-06 19:59:33.942][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv".
biodb.DEBUG[2024-05-06 19:59:33.942][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-06 19:59:33.943][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-06 19:59:33.943][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-06 19:59:33.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:33.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:33.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:33.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:33.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:33.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:33.946][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.TRACE[2024-05-06 19:59:33.946][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.947][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:33.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:33.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:33.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:33.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:33.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:33.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:33.951][FUN] Functions in observer BiodbConfig: [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[2024-05-06 19:59:33.952][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.959][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:33.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:33.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:33.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:33.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:33.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:33.969][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-05-06 19:59:33.970][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-06 19:59:33.970][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-05-06 19:59:34.018][biodb::testThat]
biodb.INFO [2024-05-06 19:59:34.018][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-06 19:59:34.018][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:34.019][biodb::testThat]
biodb.INFO [2024-05-06 19:59:34.030][biodb::testThat]
biodb.INFO [2024-05-06 19:59:34.030][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-06 19:59:34.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:34.030][biodb::testThat]
biodb.INFO [2024-05-06 19:59:34.033][biodb::testThat]
biodb.INFO [2024-05-06 19:59:34.033][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-06 19:59:34.033][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:34.033][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:34.034][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[2024-05-06 19:59:34.035][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:34.035][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-05-06 19:59:34.036][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:34.054][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.TRACE[2024-05-06 19:59:34.407][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:34.407][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:34.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:34.407][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:34.408][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:34.408][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:34.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:34.408][ef$get] fields variable is a list.
biodb.INFO [2024-05-06 19:59:34.409][biodb::testThat]
biodb.INFO [2024-05-06 19:59:34.409][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-06 19:59:34.409][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:34.409][biodb::testThat]
biodb.ERROR[2024-05-06 19:59:34.413][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-06 19:59:34.418][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-06 19:59:34.421][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-06 19:59:34.421][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-06 19:59:34.422][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-06 19:59:34.422][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-06 19:59:34.422][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.422][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.423][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-06 19:59:34.426][biodb::testContext]
biodb.INFO [2024-05-06 19:59:34.426][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:34.426][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-05-06 19:59:34.427][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:34.427][biodb::testContext]
biodb.INFO [2024-05-06 19:59:34.427][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:34.428][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:34.429][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:34.429][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-06 19:59:34.430][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-06 19:59:34.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.431][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-06 19:59:34.431][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-06 19:59:34.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.432][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-06 19:59:34.432][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-06 19:59:34.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.433][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-06 19:59:34.433][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-06 19:59:34.433][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-06 19:59:34.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.434][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-06 19:59:34.434][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-06 19:59:34.434][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-06 19:59:34.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.435][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-06 19:59:34.435][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-06 19:59:34.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.436][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-06 19:59:34.436][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-06 19:59:34.437][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-06 19:59:34.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.437][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-06 19:59:34.438][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-06 19:59:34.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.438][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-06 19:59:34.439][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-06 19:59:34.439][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-06 19:59:34.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.440][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:34.440][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-06 19:59:34.440][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-06 19:59:34.440][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-06 19:59:34.441][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-06 19:59:34.441][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-06 19:59:34.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.442][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-06 19:59:34.442][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-06 19:59:34.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.443][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-06 19:59:34.443][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-06 19:59:34.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.444][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-06 19:59:34.444][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-06 19:59:34.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.445][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-06 19:59:34.445][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-06 19:59:34.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.446][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-06 19:59:34.446][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-06 19:59:34.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.447][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:34.447][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-06 19:59:34.452][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-06 19:59:34.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.453][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[2024-05-06 19:59:34.453][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-06 19:59:34.453][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-06 19:59:34.454][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-06 19:59:34.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.455][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-06 19:59:34.455][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.456][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-06 19:59:34.456][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.456][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:34.457][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.457][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.457][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.457][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.458][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:34.458][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:34.458][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.459][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-06 19:59:34.459][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:34.459][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.459][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.460][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:34.460][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:34.460][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:34.460][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:34.460][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:34.460][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:34.460][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.461][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:34.461][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.462][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.462][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.462][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:34.462][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:34.463][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.463][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.463][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-06 19:59:34.464][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.464][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:34.464][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.465][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:34.465][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.465][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.465][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.466][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.466][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:34.466][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:34.467][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.467][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-06 19:59:34.467][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:34.467][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.468][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.468][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:34.468][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:34.468][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:34.468][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:34.468][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:34.468][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:34.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.469][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:34.469][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.470][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.470][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.470][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:34.470][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:34.471][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.471][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.471][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-06 19:59:34.472][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.472][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-06 19:59:34.473][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.473][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:34.473][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.473][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.474][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.474][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.474][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:34.474][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:34.475][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.475][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-06 19:59:34.475][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:34.476][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.476][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.476][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.483][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:34.484][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.484][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:34.484][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.485][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.485][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.485][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.485][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:34.486][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:34.486][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.486][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.486][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-06 19:59:34.487][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.487][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:34.487][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.488][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:34.488][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.488][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.488][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.489][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.489][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:34.489][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:34.489][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.490][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-06 19:59:34.490][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:34.490][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.490][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.491][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.491][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:34.491][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.492][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:34.492][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.492][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.492][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.493][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:34.493][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:34.493][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.493][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.494][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:34.494][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.494][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.DEBUG[2024-05-06 19:59:34.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.498][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[2024-05-06 19:59:34.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.512][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[2024-05-06 19:59:34.513][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-06 19:59:34.513][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-06 19:59:34.514][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-06 19:59:34.514][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-06 19:59:34.514][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-06 19:59:34.515][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-06 19:59:34.515][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:34.515][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:34.516][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-06 19:59:34.516][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-06 19:59:34.516][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-06 19:59:34.517][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-06 19:59:34.517][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:34.518][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:34.518][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-06 19:59:34.518][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-06 19:59:34.519][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-06 19:59:34.519][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-06 19:59:34.519][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-06 19:59:34.520][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-06 19:59:34.520][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-06 19:59:34.520][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-06 19:59:34.521][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-06 19:59:34.521][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-06 19:59:34.522][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-06 19:59:34.522][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-06 19:59:34.522][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-06 19:59:34.523][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-06 19:59:34.523][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-06 19:59:34.523][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-06 19:59:34.524][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-06 19:59:34.524][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-06 19:59:34.524][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-06 19:59:34.525][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-06 19:59:34.525][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-06 19:59:34.525][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-06 19:59:34.526][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-06 19:59:34.526][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-06 19:59:34.527][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-06 19:59:34.527][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-06 19:59:34.527][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-06 19:59:34.528][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-06 19:59:34.528][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-06 19:59:34.528][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-06 19:59:34.529][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-06 19:59:34.529][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-06 19:59:34.529][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-06 19:59:34.530][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-06 19:59:34.530][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-06 19:59:34.530][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-06 19:59:34.531][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-06 19:59:34.531][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-06 19:59:34.532][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-06 19:59:34.532][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-06 19:59:34.532][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-06 19:59:34.533][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-06 19:59:34.533][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-06 19:59:34.533][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-06 19:59:34.534][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-06 19:59:34.534][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-06 19:59:34.534][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-06 19:59:34.535][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-06 19:59:34.535][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-06 19:59:34.536][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-06 19:59:34.536][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-06 19:59:34.536][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-06 19:59:34.537][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-06 19:59:34.537][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-06 19:59:34.537][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-06 19:59:34.538][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-06 19:59:34.538][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-06 19:59:34.538][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-06 19:59:34.539][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-06 19:59:34.539][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-06 19:59:34.539][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-06 19:59:34.540][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-06 19:59:34.540][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-06 19:59:34.541][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-06 19:59:34.541][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-06 19:59:34.541][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-06 19:59:34.542][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-06 19:59:34.542][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-06 19:59:34.542][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-06 19:59:34.543][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-06 19:59:34.543][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:34.544][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:34.544][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.544][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.546][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[2024-05-06 19:59:34.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.574][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[2024-05-06 19:59:34.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.576][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:34.577][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-06 19:59:34.577][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.578][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.578][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.578][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:34.578][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.579][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.579][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.579][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.579][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:34.580][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:34.580][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.580][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-06 19:59:34.580][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:34.581][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:34.582][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.582][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.582][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:34.582][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.583][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.583][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.583][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-06 19:59:34.583][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-06 19:59:34.583][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:34.584][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:34.584][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.584][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.584][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-06 19:59:34.585][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-06 19:59:34.586][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-06 19:59:34.586][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-06 19:59:34.587][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-06 19:59:34.587][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-06 19:59:34.587][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-06 19:59:34.588][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-06 19:59:34.588][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-06 19:59:34.588][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-06 19:59:34.589][biodb::testThat]
biodb.INFO [2024-05-06 19:59:34.589][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-05-06 19:59:34.589][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:34.590][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:34.591][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[2024-05-06 19:59:34.592][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:34.593][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cfd52aa1c2e3525a5defd7b7e8bd8bb8".
biodb.TRACE[2024-05-06 19:59:34.593][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:34.594][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content".
biodb.DEBUG[2024-05-06 19:59:34.597][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[2024-05-06 19:59:34.598][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:34.599][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4ae22a112f570b93d2a956448ab71bd0".
biodb.TRACE[2024-05-06 19:59:34.599][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:34.600][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content".
biodb.INFO [2024-05-06 19:59:34.603][biodb::testThat]
biodb.INFO [2024-05-06 19:59:34.604][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-05-06 19:59:34.604][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:34.604][biodb::testThat]
biodb.INFO [2024-05-06 19:59:34.613][biodb::testThat]
biodb.INFO [2024-05-06 19:59:34.613][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-05-06 19:59:34.613][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:34.614][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:34.614][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[2024-05-06 19:59:34.615][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:34.616][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-05-06 19:59:34.616][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:34.617][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-05-06 19:59:34.618][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[2024-05-06 19:59:34.619][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:34.619][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-05-06 19:59:34.620][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:34.620][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-05-06 19:59:34.622][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[2024-05-06 19:59:34.623][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:34.623][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9edcc233717c530cf0cbf5f73b9c3fc7".
biodb.TRACE[2024-05-06 19:59:34.624][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:34.624][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content".
biodb.DEBUG[2024-05-06 19:59:34.626][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[2024-05-06 19:59:34.627][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:34.632][cch$loadFileContent] Trying to load 1 files from cache: [1]: "be9130a77f849b73da505cd10830451e".
biodb.TRACE[2024-05-06 19:59:34.633][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:34.637][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content".
biodb.DEBUG[2024-05-06 19:59:34.697][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[2024-05-06 19:59:34.698][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:34.698][cch$loadFileContent] Trying to load 1 files from cache: [1]: "6821b039f49696a2484834eb67daa971".
biodb.TRACE[2024-05-06 19:59:34.698][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:34.702][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content".
biodb.INFO [2024-05-06 19:59:34.762][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-06 19:59:34.762][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-06 19:59:34.763][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-06 19:59:34.763][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-06 19:59:34.763][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.764][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.764][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.764][FUN] Functions in observer BiodbConfig: [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 [2024-05-06 19:59:34.766][biodb::testContext]
biodb.INFO [2024-05-06 19:59:34.766][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:34.766][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-05-06 19:59:34.766][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-06 19:59:34.767][biodb::testContext]
biodb.INFO [2024-05-06 19:59:34.767][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:34.768][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:34.769][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:34.770][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-06 19:59:34.770][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-06 19:59:34.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.771][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-06 19:59:34.771][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-06 19:59:34.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.772][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-06 19:59:34.772][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-06 19:59:34.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.773][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-06 19:59:34.773][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-06 19:59:34.774][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-06 19:59:34.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.775][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-06 19:59:34.775][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-06 19:59:34.775][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-06 19:59:34.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.776][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-06 19:59:34.776][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-06 19:59:34.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.777][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[2024-05-06 19:59:34.777][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-06 19:59:34.777][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-06 19:59:34.778][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-06 19:59:34.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.779][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-06 19:59:34.779][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-06 19:59:34.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.780][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-06 19:59:34.780][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-06 19:59:34.780][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-06 19:59:34.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.781][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:34.781][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-06 19:59:34.782][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-06 19:59:34.782][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-06 19:59:34.782][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-06 19:59:34.782][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-06 19:59:34.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.783][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-06 19:59:34.784][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-06 19:59:34.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.784][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-06 19:59:34.785][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-06 19:59:34.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.786][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-06 19:59:34.786][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-06 19:59:34.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.787][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-06 19:59:34.787][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-06 19:59:34.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.788][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-06 19:59:34.788][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-06 19:59:34.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.789][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-06 19:59:34.789][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-06 19:59:34.794][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-06 19:59:34.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.795][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-06 19:59:34.795][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-06 19:59:34.796][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-06 19:59:34.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.797][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-06 19:59:34.797][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.797][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-06 19:59:34.798][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.798][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:34.798][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.798][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.799][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.799][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.799][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:34.799][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:34.800][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.800][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-06 19:59:34.800][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:34.800][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.801][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.801][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:34.801][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:34.801][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:34.801][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:34.801][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:34.801][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:34.802][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.802][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.802][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:34.802][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.802][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.803][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.803][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.803][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:34.803][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:34.804][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.804][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.804][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-06 19:59:34.805][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.805][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:34.805][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.805][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:34.806][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.806][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.806][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.806][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.807][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:34.807][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:34.807][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.807][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-06 19:59:34.808][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:34.808][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.808][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.808][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:34.808][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:34.808][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-06 19:59:34.808][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-06 19:59:34.808][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-06 19:59:34.809][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:34.809][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.809][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.809][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:34.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.810][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.810][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.810][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.811][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:34.811][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:34.811][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.811][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.812][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-06 19:59:34.812][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.812][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-06 19:59:34.813][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.813][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:34.813][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.813][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.814][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.814][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.814][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:34.814][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:34.815][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.815][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-06 19:59:34.815][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:34.815][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.816][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.816][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.816][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:34.816][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.817][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.817][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:34.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.817][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.818][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.818][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.818][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:34.818][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:34.819][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.819][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.819][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-06 19:59:34.820][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.820][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-06 19:59:34.820][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.820][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:34.821][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.821][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.821][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.821][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.822][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-06 19:59:34.822][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:34.822][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.822][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-06 19:59:34.823][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:34.823][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.823][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.823][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.824][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:34.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.824][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:34.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.825][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.825][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.825][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.825][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:34.826][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:34.826][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.826][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.827][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:34.827][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.837][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[2024-05-06 19:59:34.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.851][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[2024-05-06 19:59:34.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.852][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-06 19:59:34.853][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-06 19:59:34.853][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-06 19:59:34.853][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-06 19:59:34.854][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-06 19:59:34.854][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-06 19:59:34.854][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:34.855][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:34.855][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-06 19:59:34.855][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-06 19:59:34.856][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-06 19:59:34.856][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-06 19:59:34.857][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-06 19:59:34.857][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-06 19:59:34.857][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-06 19:59:34.858][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-06 19:59:34.858][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-06 19:59:34.858][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-06 19:59:34.859][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-06 19:59:34.859][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-06 19:59:34.859][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-06 19:59:34.860][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-06 19:59:34.860][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-06 19:59:34.861][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-06 19:59:34.861][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-06 19:59:34.861][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-06 19:59:34.862][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-06 19:59:34.862][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-06 19:59:34.862][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-06 19:59:34.863][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-06 19:59:34.863][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-06 19:59:34.864][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-06 19:59:34.864][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-06 19:59:34.864][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-06 19:59:34.865][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-06 19:59:34.865][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-06 19:59:34.865][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-06 19:59:34.866][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-06 19:59:34.866][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-06 19:59:34.866][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-06 19:59:34.867][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-06 19:59:34.867][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-06 19:59:34.868][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-06 19:59:34.868][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-06 19:59:34.868][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-06 19:59:34.869][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-06 19:59:34.869][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-06 19:59:34.869][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-06 19:59:34.870][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-06 19:59:34.870][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-06 19:59:34.871][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-06 19:59:34.871][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-06 19:59:34.871][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-06 19:59:34.872][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-06 19:59:34.872][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-06 19:59:34.872][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-06 19:59:34.873][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-06 19:59:34.873][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-06 19:59:34.874][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-06 19:59:34.874][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-06 19:59:34.874][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-06 19:59:34.875][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-06 19:59:34.875][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-06 19:59:34.875][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-06 19:59:34.876][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-06 19:59:34.876][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-06 19:59:34.876][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-06 19:59:34.877][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-06 19:59:34.877][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-06 19:59:34.878][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-06 19:59:34.878][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-06 19:59:34.878][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-06 19:59:34.879][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-06 19:59:34.879][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-06 19:59:34.879][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-06 19:59:34.880][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-06 19:59:34.880][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-06 19:59:34.880][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-06 19:59:34.881][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-06 19:59:34.881][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-06 19:59:34.882][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-06 19:59:34.882][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-06 19:59:34.882][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-06 19:59:34.883][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-06 19:59:34.883][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-06 19:59:34.883][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-06 19:59:34.884][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.884][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.909][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[2024-05-06 19:59:34.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-06 19:59:34.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:34.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:34.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:34.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:34.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:34.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-06 19:59:34.917][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-05-06 19:59:34.918][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-05-06 19:59:34.918][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.918][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.919][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.919][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-06 19:59:34.919][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.920][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.920][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.920][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.920][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-06 19:59:34.921][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-06 19:59:34.921][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.921][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-05-06 19:59:34.921][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-06 19:59:34.922][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-06 19:59:34.923][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.923][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-06 19:59:34.923][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-06 19:59:34.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-06 19:59:34.924][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-06 19:59:34.924][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-05-06 19:59:34.924][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-05-06 19:59:34.924][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-06 19:59:34.924][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-06 19:59:34.925][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-06 19:59:34.925][self$setPropertyValue]
biodb.DEBUG[2024-05-06 19:59:34.925][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-05-06 19:59:34.926][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-06 19:59:34.927][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-05-06 19:59:34.927][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-05-06 19:59:34.927][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-05-06 19:59:34.928][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-05-06 19:59:34.928][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-06 19:59:34.928][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-05-06 19:59:34.929][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-05-06 19:59:34.929][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-05-06 19:59:34.929][biodb::testThat]
biodb.INFO [2024-05-06 19:59:34.930][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-05-06 19:59:34.930][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-06 19:59:34.930][biodb::testThat]
biodb.DEBUG[2024-05-06 19:59:34.931][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[2024-05-06 19:59:34.933][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-06 19:59:34.933][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-05-06 19:59:34.933][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-06 19:59:34.953][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-05-06 19:59:35.315][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-05-06 19:59:35.315][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-06 19:59:35.315][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-05-06 19:59:35.316][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-06 19:59:35.316][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-05-06 19:59:35.317][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-05-06 19:59:35.317][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-05-06 19:59:35.317][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-05-06 19:59:35.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:35.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:35.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:35.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:35.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:35.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:35.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:35.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.325][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-06 19:59:35.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-06 19:59:35.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.326][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:35.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:35.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.327][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.328][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.329][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.330][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.330][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-06 19:59:35.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.331][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-06 19:59:35.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.332][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.334][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.336][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-06 19:59:35.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.337][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-06 19:59:35.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.339][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-06 19:59:35.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.344][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.345][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.346][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.347][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:35.351][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:35.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:35.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:35.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:35.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:35.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:35.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:35.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.358][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-06 19:59:35.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-06 19:59:35.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.359][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:35.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-06 19:59:35.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.360][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.361][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.362][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.363][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.364][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-06 19:59:35.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.365][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-05-06 19:59:35.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.366][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.367][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.370][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-06 19:59:35.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.371][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-05-06 19:59:35.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.373][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.374][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-05-06 19:59:35.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.380][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.381][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.383][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-06 19:59:35.392][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-05-06 19:59:35.392][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-06 19:59:35.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:35.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:35.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:35.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:35.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:35.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:35.395][FUN] Functions in observer BiodbConfig: [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[2024-05-06 19:59:35.396][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-06 19:59:35.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-06 19:59:35.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.397][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-06 19:59:35.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-06 19:59:35.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.397][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-06 19:59:35.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-06 19:59:35.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.398][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-06 19:59:35.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-06 19:59:35.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.399][private$selectFields] Fields none
biodb.TRACE[2024-05-06 19:59:35.399][private$selectFields]
biodb.TRACE[2024-05-06 19:59:35.400][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-05-06 19:59:35.400][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-06 19:59:35.400][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:35.400][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.400][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.401][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.401][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.401][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.401][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.402][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.402][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.402][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.402][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.403][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.403][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.403][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.404][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.404][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.404][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.404][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.405][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.405][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.405][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.405][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.406][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.406][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.406][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.407][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.407][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.407][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.408][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.408][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.408][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.408][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.409][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.409][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.409][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.409][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.410][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.410][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.410][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.411][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.411][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.411][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.411][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.412][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.412][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.412][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.413][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.413][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.413][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.414][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.414][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:35.414][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:35.414][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.415][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.415][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.415][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.415][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.416][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.416][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.416][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.417][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.417][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.417][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.418][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.418][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.418][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.418][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.419][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.419][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.419][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.419][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.420][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.420][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.420][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.421][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.421][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.421][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-05-06 19:59:35.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.427][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.428][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.428][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.429][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.430][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.431][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.435][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.435][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.441][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.443][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.444][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.445][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.446][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.448][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-05-06 19:59:35.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-06 19:59:35.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:35.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:35.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:35.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:35.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:35.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-06 19:59:35.452][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-06 19:59:35.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-06 19:59:35.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.453][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-06 19:59:35.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-06 19:59:35.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.454][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-06 19:59:35.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-06 19:59:35.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.454][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-06 19:59:35.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-06 19:59:35.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.455][private$selectFields] Fields none
biodb.TRACE[2024-05-06 19:59:35.455][private$selectFields]
biodb.TRACE[2024-05-06 19:59:35.456][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-05-06 19:59:35.456][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-06 19:59:35.456][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:35.456][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.457][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.457][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.457][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.457][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.458][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.458][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.458][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.459][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.459][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.459][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.459][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.460][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.460][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.460][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.461][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.461][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.461][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.461][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.462][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.462][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.462][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.462][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.463][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.463][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.463][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.464][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.464][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.464][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.464][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.465][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.465][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.465][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.466][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.466][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.466][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.466][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.467][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.467][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.467][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.467][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.468][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.468][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.468][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.469][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.469][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.469][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.470][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.470][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:35.470][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-05-06 19:59:35.470][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.470][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.471][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.471][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.471][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.472][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.472][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.472][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.473][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.473][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.473][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.473][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.474][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.474][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.474][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.474][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.475][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.475][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.475][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.476][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.476][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.476][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.476][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.477][ef$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.477][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-05-06 19:59:35.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-06 19:59:35.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-06 19:59:35.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-06 19:59:35.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.483][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.483][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.484][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-06 19:59:35.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.485][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.486][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.487][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-06 19:59:35.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-06 19:59:35.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.491][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.492][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-06 19:59:35.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-06 19:59:35.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-06 19:59:35.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-06 19:59:35.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.496][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.497][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.502][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-05-06 19:59:35.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-06 19:59:35.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-06 19:59:35.504][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-05-06 19:59:35.504][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-05-06 19:59:35.505][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-05-06 19:59:35.506][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-06 19:59:35.507][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-05-06 19:59:35.507][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-05-06 19:59:35.507][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-06 19:59:35.507][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-06 19:59:35.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-06 19:59:35.508][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-06 19:59:35.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-06 19:59:35.508][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-06 19:59:35.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 161 ]

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

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

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

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 161 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn0.5960.2000.797
LipidmapsStructureEntry0.1030.0050.109