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This page was generated on 2024-06-28 17:44 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_19
git_last_commit: 323ed25
git_last_commit_date: 2024-04-30 11:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  

CHECK results for biodbLipidmaps on kjohnson1

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

raw results


Summary

Package: biodbLipidmaps
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-06-27 12:48:33 -0400 (Thu, 27 Jun 2024)
EndedAt: 2024-06-27 12:51:08 -0400 (Thu, 27 Jun 2024)
EllapsedTime: 155.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.0 (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 13.6.6
* 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 166 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

Installation output

biodbLipidmaps.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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 [2024-06-27 12:49:23.943][biodb::testContext]
biodb.INFO [2024-06-27 12:49:23.948][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 12:49:23.949][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-27 12:49:23.950][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 12:49:23.951][biodb::testContext]
biodb.INFO [2024-06-27 12:49:23.960][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-27 12:49:23.962][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-27 12:49:23.972][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 12:49:23.974][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-27 12:49:23.975][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-27 12:49:23.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:23.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:23.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:23.978][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-27 12:49:24.014][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-27 12:49:24.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.018][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-27 12:49:24.019][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-27 12:49:24.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.022][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-27 12:49:24.022][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-27 12:49:24.023][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-27 12:49:24.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.026][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-27 12:49:24.027][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-27 12:49:24.028][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-27 12:49:24.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.031][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-27 12:49:24.032][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-27 12:49:24.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.034][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-27 12:49:24.035][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-27 12:49:24.036][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-27 12:49:24.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.039][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-27 12:49:24.040][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-27 12:49:24.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.043][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-27 12:49:24.044][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-27 12:49:24.044][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-27 12:49:24.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.047][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-27 12:49:24.048][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-27 12:49:24.049][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-27 12:49:24.050][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-27 12:49:24.051][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-27 12:49:24.051][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-27 12:49:24.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.055][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-27 12:49:24.055][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-27 12:49:24.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.058][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-27 12:49:24.059][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-27 12:49:24.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.062][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-27 12:49:24.063][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-27 12:49:24.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.066][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-27 12:49:24.066][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-27 12:49:24.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.069][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-27 12:49:24.070][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-27 12:49:24.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.073][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-27 12:49:24.074][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-27 12:49:24.089][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-27 12:49:24.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.092][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-27 12:49:24.093][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-27 12:49:24.094][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-27 12:49:24.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.101][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-27 12:49:24.136][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.151][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-27 12:49:24.152][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.153][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:49:24.154][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.155][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.156][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.157][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.157][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 12:49:24.158][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:49:24.159][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.160][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-27 12:49:24.161][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:49:24.161][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.162][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.163][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 12:49:24.163][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 12:49:24.163][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 12:49:24.163][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 12:49:24.163][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 12:49:24.164][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:49:24.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:49:24.166][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:49:24.166][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:49:24.167][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:49:24.168][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:49:24.169][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.169][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.170][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:49:24.171][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:49:24.172][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.172][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.173][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-27 12:49:24.175][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.176][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 12:49:24.177][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.178][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:49:24.178][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.179][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.180][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.181][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.182][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 12:49:24.182][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:49:24.183][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.184][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-27 12:49:24.185][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:49:24.193][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.194][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.195][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 12:49:24.195][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 12:49:24.195][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 12:49:24.195][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 12:49:24.195][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 12:49:24.196][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:49:24.197][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:49:24.198][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:49:24.199][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:49:24.200][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:49:24.201][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:49:24.202][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.203][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.204][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:49:24.204][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:49:24.205][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.206][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.207][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-27 12:49:24.209][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.210][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-27 12:49:24.211][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.212][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:49:24.213][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.214][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.215][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.216][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.217][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 12:49:24.217][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:49:24.218][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.219][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-27 12:49:24.220][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:49:24.221][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.222][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.222][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.223][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:49:24.224][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:49:24.225][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:49:24.226][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:49:24.226][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:49:24.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:49:24.228][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.229][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.230][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:49:24.230][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:49:24.231][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.232][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.233][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-27 12:49:24.235][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.236][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 12:49:24.237][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.238][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:49:24.238][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.239][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.240][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.241][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.242][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 12:49:24.243][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:49:24.244][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.244][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-27 12:49:24.245][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:49:24.246][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.247][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.248][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.248][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:49:24.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:49:24.250][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:49:24.251][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:49:24.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:49:24.253][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:49:24.254][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.255][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.256][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:49:24.257][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:49:24.258][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.258][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.263][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 12:49:24.264][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.265][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[2024-06-27 12:49:24.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.269][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[2024-06-27 12:49:24.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.272][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[2024-06-27 12:49:24.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.286][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[2024-06-27 12:49:24.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.310][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.DEBUG[2024-06-27 12:49:24.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.324][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-27 12:49:24.330][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-27 12:49:24.332][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-27 12:49:24.333][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-27 12:49:24.334][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-27 12:49:24.335][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-27 12:49:24.336][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-27 12:49:24.337][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-27 12:49:24.338][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-27 12:49:24.340][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-27 12:49:24.341][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-27 12:49:24.342][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-27 12:49:24.343][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-27 12:49:24.344][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-27 12:49:24.345][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-27 12:49:24.346][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-27 12:49:24.348][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-27 12:49:24.349][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-27 12:49:24.350][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-27 12:49:24.351][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-27 12:49:24.358][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-27 12:49:24.360][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-27 12:49:24.361][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-27 12:49:24.362][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-27 12:49:24.363][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-27 12:49:24.364][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-27 12:49:24.365][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-27 12:49:24.367][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-27 12:49:24.368][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-27 12:49:24.369][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-27 12:49:24.370][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-27 12:49:24.371][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-27 12:49:24.373][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-27 12:49:24.374][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-27 12:49:24.375][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-27 12:49:24.376][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-27 12:49:24.377][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-27 12:49:24.378][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-27 12:49:24.380][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-27 12:49:24.381][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-27 12:49:24.382][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-27 12:49:24.383][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-27 12:49:24.384][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-27 12:49:24.385][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-27 12:49:24.386][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-27 12:49:24.388][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-27 12:49:24.389][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-27 12:49:24.390][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-27 12:49:24.391][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-27 12:49:24.392][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-27 12:49:24.393][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-27 12:49:24.394][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-27 12:49:24.396][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-27 12:49:24.397][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-27 12:49:24.398][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-27 12:49:24.399][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-27 12:49:24.400][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-27 12:49:24.401][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-27 12:49:24.402][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-27 12:49:24.403][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-27 12:49:24.404][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-27 12:49:24.406][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-27 12:49:24.407][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-27 12:49:24.408][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-27 12:49:24.409][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-27 12:49:24.410][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-27 12:49:24.411][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-27 12:49:24.412][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-27 12:49:24.413][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-27 12:49:24.414][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-27 12:49:24.415][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-27 12:49:24.417][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-27 12:49:24.418][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-27 12:49:24.419][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-27 12:49:24.420][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-27 12:49:24.421][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-27 12:49:24.422][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-27 12:49:24.423][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-27 12:49:24.424][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-27 12:49:24.425][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-27 12:49:24.426][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-27 12:49:24.428][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-27 12:49:24.430][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-27 12:49:24.437][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-27 12:49:24.439][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-27 12:49:24.443][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 12:49:24.444][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.446][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.447][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[2024-06-27 12:49:24.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.498][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[2024-06-27 12:49:24.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.503][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[2024-06-27 12:49:24.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.507][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[2024-06-27 12:49:24.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:24.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:49:24.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.546][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[2024-06-27 12:49:24.548][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-27 12:49:24.559][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-27 12:49:24.561][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.562][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.563][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.564][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:49:24.564][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.565][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.566][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.567][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.568][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 12:49:24.569][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:49:24.570][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.570][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-27 12:49:24.571][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:49:24.572][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-27 12:49:24.572][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-27 12:49:24.572][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-27 12:49:24.572][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-27 12:49:24.572][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-27 12:49:24.572][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-27 12:49:24.572][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-27 12:49:24.572][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-27 12:49:24.572][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-27 12:49:24.573][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-27 12:49:24.574][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 12:49:24.574][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 12:49:24.575][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:49:24.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:49:24.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:49:24.577][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:49:24.578][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:49:24.578][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:49:24.579][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:49:24.580][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-27 12:49:24.580][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-27 12:49:24.581][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:49:24.582][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:49:24.583][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-27 12:49:24.584][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:49:24.590][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-27 12:49:24.592][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-27 12:49:24.623][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-27 12:49:24.625][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-27 12:49:24.630][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-27 12:49:24.636][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-27 12:49:24.641][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-27 12:49:24.642][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-27 12:49:24.644][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-27 12:49:24.645][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-27 12:49:24.658][biodb::testThat]
biodb.INFO [2024-06-27 12:49:24.659][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-27 12:49:24.660][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:49:24.661][biodb::testThat]
biodb.TRACE[2024-06-27 12:49:24.666][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[2024-06-27 12:49:24.668][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-27 12:49:24.673][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-27 12:49:24.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:49:24.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:24.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:24.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:24.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:24.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:24.702][FUN] Functions in observer BiodbConfig: [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[2024-06-27 12:49:24.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:24.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:24.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:24.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:24.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:49:24.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:49:24.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.755][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-27 12:49:24.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-27 12:49:24.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.758][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 12:49:24.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 12:49:24.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.762][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:24.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:24.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.790][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:24.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:24.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.794][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:24.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:24.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.798][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:24.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:24.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.802][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-27 12:49:24.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:24.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.805][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-27 12:49:24.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:24.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.809][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:24.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:24.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.812][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:24.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:24.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:24.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:24.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:24.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:24.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.822][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-27 12:49:24.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:24.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.826][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-27 12:49:24.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:24.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:24.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:24.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:24.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:24.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.836][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-27 12:49:24.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:24.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:24.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:24.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:24.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:24.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:24.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:24.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:24.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:24.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:24.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:24.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.955][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:24.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:24.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.958][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:24.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:24.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:24.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:24.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.965][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:24.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:24.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:24.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:24.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:24.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:24.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:24.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:24.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:24.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:24.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:24.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:24.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:24.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:24.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:49:24.990][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-27 12:49:24.993][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 12:49:24.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 12:49:24.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:24.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:24.997][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 12:49:24.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 12:49:24.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.001][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-27 12:49:25.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-27 12:49:25.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.004][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-27 12:49:25.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-27 12:49:25.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.046][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.087][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.090][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.094][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.121][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.122][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.123][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.148][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.149][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.151][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.164][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.168][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.172][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.175][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.176][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.178][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.190][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:25.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:25.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.194][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:25.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:25.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.198][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:25.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:25.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.201][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:25.202][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:25.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.204][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.204][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:25.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:25.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.235][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.236][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.238][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.251][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.255][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.259][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.262][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.264][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.265][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.266][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.278][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.280][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.281][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.287][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.288][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.290][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.295][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:25.296][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:25.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.298][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.304][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.305][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.307][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.313][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.314][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.316][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.321][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.322][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.324][ef$get] fields variable is a list.
biodb.INFO [2024-06-27 12:49:25.332][biodb::testThat]
biodb.INFO [2024-06-27 12:49:25.333][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-27 12:49:25.334][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:49:25.335][biodb::testThat]
biodb.DEBUG[2024-06-27 12:49:25.351][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-06-27 12:49:25.361][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 12:49:25.366][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-06-27 12:49:25.368][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 12:49:25.369][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-06-27 12:49:25.370][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 12:49:25.402][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-27 12:49:25.403][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-27 12:49:25.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:49:25.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:25.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:25.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:25.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:25.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:25.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:49:25.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:49:25.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:49:25.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:49:25.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:49:25.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.434][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-27 12:49:25.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-27 12:49:25.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.438][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 12:49:25.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 12:49:25.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.442][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.446][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:25.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.449][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.453][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:25.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.456][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-27 12:49:25.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.459][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-27 12:49:25.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:25.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.463][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:25.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:25.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.466][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:25.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:25.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.477][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-27 12:49:25.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.481][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-27 12:49:25.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.484][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.491][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-27 12:49:25.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.507][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.511][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.514][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.521][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:25.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:25.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:25.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:49:25.551][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-27 12:49:25.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-27 12:49:25.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-27 12:49:25.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-27 12:49:25.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-27 12:49:25.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-27 12:49:25.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-27 12:49:25.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-27 12:49:25.571][biodb::testThat]
biodb.INFO [2024-06-27 12:49:25.572][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-27 12:49:25.573][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:49:25.574][biodb::testThat]
biodb.TRACE[2024-06-27 12:49:25.578][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.579][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.581][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:49:25.582][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-06-27 12:49:25.610][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:25.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:25.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:25.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:25.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:49:25.625][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-27 12:49:25.632][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[2024-06-27 12:49:25.653][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:49:25.655][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 12:49:25.656][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-06-27 12:49:26.091][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-06-27 12:49:26.384][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:49:26.387][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-06-27 12:49:26.402][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-06-27 12:49:26.404][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-06-27 12:49:26.416][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:26.417][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:26.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:26.419][ef$get] fields variable is a list.
biodb.INFO [2024-06-27 12:49:26.436][biodb::testThat]
biodb.INFO [2024-06-27 12:49:26.437][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-27 12:49:26.438][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:49:26.439][biodb::testThat]
biodb.TRACE[2024-06-27 12:49:26.463][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:26.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:26.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:26.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:26.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:26.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:26.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:26.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:26.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:26.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:26.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:26.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:49:26.579][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-27 12:49:26.583][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 12:49:26.598][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-27 12:49:26.599][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 12:49:26.601][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-06-27 12:49:26.616][biodb::testThat]
biodb.INFO [2024-06-27 12:49:26.617][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-27 12:49:26.618][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:49:26.619][biodb::testThat]
biodb.TRACE[2024-06-27 12:49:26.645][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 12:49:26.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 12:49:26.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:26.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:26.649][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 12:49:26.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 12:49:26.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:26.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:26.652][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-27 12:49:26.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-27 12:49:26.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:26.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:26.656][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-27 12:49:26.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-27 12:49:26.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:26.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:26.698][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 12:49:26.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 12:49:26.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:26.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:26.702][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 12:49:26.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 12:49:26.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:26.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:26.705][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-27 12:49:26.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-27 12:49:26.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:26.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:26.708][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-27 12:49:26.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-27 12:49:26.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:26.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-27 12:49:26.718][biodb::testThat]
biodb.INFO [2024-06-27 12:49:26.719][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-27 12:49:26.719][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:49:26.720][biodb::testThat]
biodb.INFO [2024-06-27 12:49:26.734][biodb::testThat]
biodb.INFO [2024-06-27 12:49:26.735][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-27 12:49:26.735][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:49:26.736][biodb::testThat]
biodb.INFO [2024-06-27 12:49:26.744][biodb::testThat]
biodb.INFO [2024-06-27 12:49:26.745][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-27 12:49:26.745][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:49:26.746][biodb::testThat]
biodb.DEBUG[2024-06-27 12:49:26.750][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-06-27 12:49:27.081][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-06-27 12:49:27.169][biodb::testThat]
biodb.INFO [2024-06-27 12:49:27.170][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-27 12:49:27.171][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:49:27.172][biodb::testThat]
biodb.TRACE[2024-06-27 12:49:27.178][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:27.179][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:27.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:27.181][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:27.181][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:27.182][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:27.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:27.184][ef$get] fields variable is a list.
biodb.INFO [2024-06-27 12:49:27.186][biodb::testThat]
biodb.INFO [2024-06-27 12:49:27.186][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-27 12:49:27.187][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:49:27.188][biodb::testThat]
biodb.TRACE[2024-06-27 12:49:27.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:27.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:27.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:27.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:27.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:27.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:27.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:27.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:27.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:27.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:27.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:27.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:49:27.296][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-27 12:49:27.300][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 12:49:27.301][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-27 12:49:27.302][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 12:49:27.304][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-06-27 12:49:27.369][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-27 12:49:27.373][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 12:49:27.374][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-27 12:49:27.375][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 12:49:27.376][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-06-27 12:49:27.391][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-27 12:49:27.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-27 12:49:27.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:27.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:27.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 12:49:27.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 12:49:27.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:27.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:27.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:27.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:27.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:27.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:27.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:27.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:27.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:27.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:27.413][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:27.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:27.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:27.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:27.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:27.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:27.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:27.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:27.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:27.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:27.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:27.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:49:27.430][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-27 12:49:27.447][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:49:27.448][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 12:49:27.470][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-27 12:49:31.075][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-27 12:49:36.346][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:49:36.349][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-06-27 12:49:36.361][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-06-27 12:49:37.737][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[2024-06-27 12:49:37.740][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:49:37.741][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 12:49:37.743][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-27 12:49:38.050][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-27 12:49:38.343][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:49:38.345][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-06-27 12:49:38.349][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-06-27 12:49:38.370][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-06-27 12:49:38.374][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:49:38.375][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:49:38.376][rule$waitAsNeeded] Wait 0.366447 second(s).
biodb.TRACE[2024-06-27 12:49:38.855][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-06-27 12:49:39.153][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-06-27 12:49:39.465][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:49:39.467][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-06-27 12:49:39.471][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-06-27 12:49:39.487][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-27 12:49:39.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-27 12:49:39.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:39.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-27 12:49:39.498][biodb::testThat]
biodb.INFO [2024-06-27 12:49:39.499][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-27 12:49:39.500][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:49:39.500][biodb::testThat]
biodb.TRACE[2024-06-27 12:49:39.503][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-27 12:49:39.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-27 12:49:39.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:39.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:39.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 12:49:39.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 12:49:39.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:39.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:39.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:39.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:39.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:39.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:39.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:39.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:39.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:39.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:39.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:39.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:39.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:39.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:39.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:39.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:39.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:39.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:49:39.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:49:39.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:39.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:39.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:39.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:39.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:39.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:39.543][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-06-27 12:49:39.548][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:49:39.549][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:49:39.550][rule$waitAsNeeded] Wait 0.303723 second(s).
biodb.TRACE[2024-06-27 12:49:39.918][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-06-27 12:49:43.646][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-06-27 12:49:48.047][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:49:48.049][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-06-27 12:49:48.058][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-06-27 12:49:49.624][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-06-27 12:49:49.668][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-27 12:49:49.671][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-06-27 12:49:49.672][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-27 12:49:49.673][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 12:49:49.674][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 12:49:49.675][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-27 12:49:49.676][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 12:49:49.676][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 12:49:49.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:49:49.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:49.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:49.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:49.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:49.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:49.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:49.703][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-06-27 12:49:49.706][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:49:49.707][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 12:49:49.708][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-27 12:49:50.025][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-06-27 12:49:50.345][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:49:50.348][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-06-27 12:49:50.352][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-06-27 12:49:50.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:49:50.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:50.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:50.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:50.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:50.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:50.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:50.366][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-06-27 12:49:50.370][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:49:50.371][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:49:50.372][rule$waitAsNeeded] Wait 0.335865 second(s).
biodb.TRACE[2024-06-27 12:49:50.710][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-06-27 12:49:51.024][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-06-27 12:49:51.348][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:49:51.351][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-06-27 12:49:51.355][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-06-27 12:49:51.358][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-06-27 12:49:51.360][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 12:49:51.361][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-27 12:49:51.363][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-27 12:49:51.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:49:51.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:51.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:51.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:51.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:51.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:51.376][FUN] Functions in observer BiodbConfig: [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[2024-06-27 12:49:51.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:49:51.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:49:51.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:49:51.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:49:51.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.398][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-27 12:49:51.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-27 12:49:51.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.403][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 12:49:51.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 12:49:51.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.406][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:51.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:51.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.410][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:51.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:51.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.414][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:51.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:51.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.418][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:51.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:51.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.422][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-27 12:49:51.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:51.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.425][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-27 12:49:51.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:51.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.430][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:51.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:51.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.433][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:51.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:51.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:51.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.441][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:51.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.446][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-27 12:49:51.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.450][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-27 12:49:51.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:51.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:51.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.461][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-27 12:49:51.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.465][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.469][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.476][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:49:51.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:49:51.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:51.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:51.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:51.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:51.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:51.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:49:51.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:49:51.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:49:51.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.520][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-27 12:49:51.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-27 12:49:51.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.524][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 12:49:51.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 12:49:51.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.528][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:51.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:51.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.532][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:51.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:49:51.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:51.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:51.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.562][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:51.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:49:51.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.565][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-27 12:49:51.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:51.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.569][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-27 12:49:51.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:51.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.572][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:51.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:51.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.575][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:49:51.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:49:51.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:51.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:51.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.586][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-27 12:49:51.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.590][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-27 12:49:51.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:51.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.596][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:49:51.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.599][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-27 12:49:51.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:49:51.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.603][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.606][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.612][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:49:51.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:49:51.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:49:51.646][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-06-27 12:49:51.655][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-27 12:49:51.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:49:51.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:51.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:51.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:51.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:51.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:51.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:49:51.669][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.672][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.676][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:49:51.676][private$selectFields]
biodb.TRACE[2024-06-27 12:49:51.677][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 12:49:51.678][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 12:49:51.679][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:49:51.680][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.681][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.682][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.683][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.684][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.685][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.686][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:49:51.687][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:49:51.687][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.688][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.690][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.691][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-27 12:49:51.692][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.695][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.698][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.711][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-27 12:49:51.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:49:51.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:51.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:51.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:51.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:51.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:51.723][FUN] Functions in observer BiodbConfig: [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[2024-06-27 12:49:51.724][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.727][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.731][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:49:51.732][private$selectFields]
biodb.TRACE[2024-06-27 12:49:51.732][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 12:49:51.733][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 12:49:51.734][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:49:51.735][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.736][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.737][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.738][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.739][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.741][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.742][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:49:51.743][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:49:51.743][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.744][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.746][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.747][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-27 12:49:51.748][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.751][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.755][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.759][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-27 12:49:51.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:49:51.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:51.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:51.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:51.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:51.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:51.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:49:51.772][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.776][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.779][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:49:51.780][private$selectFields]
biodb.TRACE[2024-06-27 12:49:51.781][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 12:49:51.781][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 12:49:51.782][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:49:51.783][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.784][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.786][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.787][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.788][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.789][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.790][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:49:51.791][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:49:51.792][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.792][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.794][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.795][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-27 12:49:51.796][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.799][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.803][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:49:51.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.806][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-27 12:49:51.807][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-27 12:49:51.808][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-27 12:49:51.819][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-27 12:49:51.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-27 12:49:51.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-27 12:49:51.827][biodb::testThat]
biodb.INFO [2024-06-27 12:49:51.828][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-27 12:49:51.829][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:49:51.830][biodb::testThat]
biodb.TRACE[2024-06-27 12:49:51.834][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-27 12:49:51.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-27 12:49:51.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 12:49:51.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 12:49:51.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:51.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:51.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:51.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:51.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:51.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:51.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:49:51.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:51.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:49:51.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:49:51.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:49:51.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:49:51.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:49:51.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:49:51.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:49:51.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:49:51.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:49:51.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:49:51.938][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-06-27 12:49:51.942][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:49:51.943][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 12:49:51.945][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-06-27 12:49:55.593][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-06-27 12:50:00.475][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:50:00.480][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-06-27 12:50:00.491][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-06-27 12:50:02.052][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-27 12:50:02.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:02.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:02.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:02.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:02.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:02.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:02.085][FUN] Functions in observer BiodbConfig: [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[2024-06-27 12:50:02.097][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.101][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.123][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:02.125][private$selectFields]
biodb.TRACE[2024-06-27 12:50:02.126][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 12:50:02.126][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 12:50:02.127][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:02.128][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.129][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.131][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.132][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.133][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.134][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.135][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:02.146][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:02.147][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.148][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.150][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.151][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-27 12:50:02.151][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.155][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.159][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.164][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-27 12:50:02.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:02.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:02.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:02.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:02.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:02.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:02.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:50:02.178][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.182][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.185][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:02.186][private$selectFields]
biodb.TRACE[2024-06-27 12:50:02.187][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 12:50:02.188][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 12:50:02.189][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:02.190][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.191][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.193][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.193][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.194][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.196][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.197][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:02.198][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:02.199][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.201][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.203][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.204][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-27 12:50:02.205][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.208][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.212][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.216][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-27 12:50:02.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:02.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:02.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:02.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:02.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:02.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:02.228][FUN] Functions in observer BiodbConfig: [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[2024-06-27 12:50:02.230][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.234][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.237][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:02.238][private$selectFields]
biodb.TRACE[2024-06-27 12:50:02.239][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 12:50:02.240][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 12:50:02.241][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:02.241][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.242][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.244][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.245][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.246][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.248][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.248][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:02.249][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:02.250][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.251][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.253][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.254][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-27 12:50:02.255][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.260][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.263][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:02.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.267][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-27 12:50:02.268][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-27 12:50:02.269][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-27 12:50:02.279][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-27 12:50:02.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-27 12:50:02.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-27 12:50:02.287][biodb::testThat]
biodb.INFO [2024-06-27 12:50:02.288][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-27 12:50:02.289][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:50:02.290][biodb::testThat]
biodb.TRACE[2024-06-27 12:50:02.293][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-27 12:50:02.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-27 12:50:02.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-27 12:50:02.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-27 12:50:02.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:02.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:02.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:02.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:02.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:02.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:02.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:02.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:02.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:02.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:02.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:50:02.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:02.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:02.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:02.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:02.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:02.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:02.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:02.601][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[2024-06-27 12:50:02.605][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 12:50:02.606][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-06-27 12:50:02.608][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 12:50:02.672][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-06-27 12:50:03.929][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-27 12:50:03.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:03.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:03.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:03.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:03.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:03.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:03.940][FUN] Functions in observer BiodbConfig: [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[2024-06-27 12:50:03.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:03.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:03.946][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:03.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:03.949][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:03.950][private$selectFields]
biodb.TRACE[2024-06-27 12:50:03.951][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 12:50:03.952][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 12:50:03.952][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:03.953][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.954][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:03.956][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:03.956][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.957][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:03.959][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:03.960][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:03.961][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:03.961][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.962][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:03.964][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:03.964][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-27 12:50:03.965][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:03.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:03.970][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:03.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:03.973][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:03.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:03.976][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-27 12:50:03.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:03.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:03.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:03.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:03.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:03.986][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:03.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:50:03.988][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:03.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:03.992][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:03.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:03.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:03.996][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:03.997][private$selectFields]
biodb.TRACE[2024-06-27 12:50:03.998][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 12:50:03.999][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 12:50:03.999][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:04.000][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.001][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.003][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.003][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.004][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.006][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.007][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:04.007][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:04.008][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.009][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.012][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.013][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-27 12:50:04.014][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.017][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.020][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.024][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-27 12:50:04.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:04.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:04.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:04.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:04.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:04.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:04.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:50:04.037][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.041][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.044][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:04.045][private$selectFields]
biodb.TRACE[2024-06-27 12:50:04.046][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-27 12:50:04.046][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 12:50:04.048][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:04.049][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.050][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.051][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.052][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.053][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.055][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.056][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:04.056][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:04.058][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.059][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.061][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.062][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-27 12:50:04.062][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.066][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.069][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:04.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:04.072][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-27 12:50:04.074][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-27 12:50:04.075][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-27 12:50:04.098][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-27 12:50:04.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-27 12:50:04.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:04.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-27 12:50:04.106][biodb::testThat]
biodb.INFO [2024-06-27 12:50:04.107][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-27 12:50:04.108][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:50:04.109][biodb::testThat]
biodb.DEBUG[2024-06-27 12:50:04.111][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-27 12:50:04.112][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-27 12:50:04.113][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-27 12:50:04.115][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-27 12:50:04.116][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 12:50:04.117][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 12:50:04.118][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-27 12:50:04.119][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 12:50:04.120][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 12:50:04.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:04.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:04.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:04.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:04.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:04.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:04.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:04.146][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-06-27 12:50:04.149][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:04.150][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 12:50:04.151][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-27 12:50:04.414][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:04.414][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:04.415][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:04.415][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-27 12:50:04.676][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:04.677][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:04.677][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:04.678][rule$waitAsNeeded] Wait 0.473522 second(s).
biodb.TRACE[2024-06-27 12:50:05.173][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-27 12:50:05.477][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:05.479][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:05.480][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:05.481][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-27 12:50:06.016][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:06.017][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:06.018][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:06.019][rule$waitAsNeeded] Wait 0.15355 second(s).
biodb.TRACE[2024-06-27 12:50:06.325][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-27 12:50:06.600][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:06.601][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:06.602][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:06.603][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-27 12:50:06.865][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:06.866][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:06.868][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:06.869][rule$waitAsNeeded] Wait 0.45526 second(s).
biodb.TRACE[2024-06-27 12:50:07.476][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-27 12:50:07.760][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:07.761][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:07.762][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:07.763][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-27 12:50:08.308][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:08.309][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:08.310][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:08.311][rule$waitAsNeeded] Wait 0.164597 second(s).
biodb.TRACE[2024-06-27 12:50:08.627][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-27 12:50:08.922][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:08.924][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:08.925][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:08.926][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-27 12:50:09.220][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:09.221][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:09.222][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:09.223][rule$waitAsNeeded] Wait 0.403756 second(s).
biodb.TRACE[2024-06-27 12:50:09.767][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-27 12:50:10.057][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:10.058][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:10.060][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:10.061][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-27 12:50:10.347][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:10.348][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:10.349][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:10.350][rule$waitAsNeeded] Wait 0.416202 second(s).
biodb.TRACE[2024-06-27 12:50:10.918][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-27 12:50:11.204][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:11.205][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:11.206][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:11.207][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-27 12:50:11.442][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:11.443][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:11.444][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:11.445][rule$waitAsNeeded] Wait 0.472513 second(s).
biodb.TRACE[2024-06-27 12:50:12.018][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-27 12:50:12.272][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:12.273][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:12.274][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:12.275][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-27 12:50:12.519][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:12.520][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:12.521][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:12.522][rule$waitAsNeeded] Wait 0.495787 second(s).
biodb.TRACE[2024-06-27 12:50:13.169][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-27 12:50:13.412][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:13.443][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:13.444][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:13.445][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-27 12:50:13.685][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:13.686][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:13.687][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:13.688][rule$waitAsNeeded] Wait 0.481098 second(s).
biodb.TRACE[2024-06-27 12:50:14.320][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-27 12:50:14.572][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:14.573][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:14.574][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:14.575][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-27 12:50:14.817][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-27 12:50:14.819][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-06-27 12:50:14.821][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 12:50:14.822][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-27 12:50:14.823][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-27 12:50:14.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:14.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:14.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:14.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:14.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:14.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:14.834][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.TRACE[2024-06-27 12:50:14.836][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:14.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:14.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:14.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:14.839][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:14.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:14.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:14.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:14.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:14.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:14.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:14.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:14.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:14.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:14.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:14.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:14.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:14.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:14.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:14.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:14.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:14.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:14.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:14.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:14.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:14.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:14.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:14.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:14.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:14.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:14.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:14.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:50:14.860][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-06-27 12:50:14.861][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-27 12:50:14.869][biodb::testThat]
biodb.INFO [2024-06-27 12:50:14.870][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-27 12:50:14.871][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:50:14.872][biodb::testThat]
biodb.DEBUG[2024-06-27 12:50:14.881][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-06-27 12:50:14.883][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-06-27 12:50:14.884][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-27 12:50:14.886][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-06-27 12:50:14.887][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-27 12:50:14.888][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-27 12:50:14.889][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 12:50:14.890][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-27 12:50:14.891][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-27 12:50:14.892][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-27 12:50:14.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:14.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:14.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:14.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:14.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:14.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:14.906][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[2024-06-27 12:50:14.907][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-06-27 12:50:14.910][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:14.911][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:14.912][rule$waitAsNeeded] Wait 0.407864 second(s).
biodb.TRACE[2024-06-27 12:50:15.352][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-27 12:50:15.596][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:15.597][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:15.598][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:15.599][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-27 12:50:15.797][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:15.798][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:15.799][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:15.800][rule$waitAsNeeded] Wait 0.551623 second(s).
biodb.TRACE[2024-06-27 12:50:16.503][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-27 12:50:16.750][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:16.752][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:16.753][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:16.754][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-27 12:50:17.241][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:17.242][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:17.243][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:17.244][rule$waitAsNeeded] Wait 0.258772 second(s).
biodb.TRACE[2024-06-27 12:50:17.517][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-27 12:50:17.759][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:17.760][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:17.761][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:17.762][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-27 12:50:18.255][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:18.256][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:18.257][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:18.258][rule$waitAsNeeded] Wait 0.258544 second(s).
biodb.TRACE[2024-06-27 12:50:18.529][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-27 12:50:18.765][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:18.766][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:18.767][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:18.768][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-27 12:50:19.144][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:19.146][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:19.146][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:19.147][rule$waitAsNeeded] Wait 0.381092 second(s).
biodb.TRACE[2024-06-27 12:50:19.680][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-27 12:50:19.918][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:19.919][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:19.921][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:19.921][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-27 12:50:20.417][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:20.418][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:20.419][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:20.420][rule$waitAsNeeded] Wait 0.259322 second(s).
biodb.TRACE[2024-06-27 12:50:20.831][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-27 12:50:21.053][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:21.054][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:21.055][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:21.056][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-27 12:50:21.544][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:21.545][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:21.546][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:21.547][rule$waitAsNeeded] Wait 0.283904 second(s).
biodb.TRACE[2024-06-27 12:50:21.982][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-27 12:50:22.231][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:22.232][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:22.233][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:22.234][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-27 12:50:22.520][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:22.521][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:22.522][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:22.523][rule$waitAsNeeded] Wait 0.458861 second(s).
biodb.TRACE[2024-06-27 12:50:22.986][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-27 12:50:23.239][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:23.240][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:23.241][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:23.242][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-27 12:50:23.477][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:23.478][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:23.479][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:23.480][rule$waitAsNeeded] Wait 0.505821 second(s).
biodb.TRACE[2024-06-27 12:50:24.137][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-27 12:50:24.370][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:24.371][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:24.372][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:24.373][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-27 12:50:24.609][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:24.610][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:24.611][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:24.613][rule$waitAsNeeded] Wait 0.524513 second(s).
biodb.TRACE[2024-06-27 12:50:25.289][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-27 12:50:25.539][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:25.540][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:25.541][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:25.542][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-27 12:50:25.788][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:25.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:25.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:25.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:25.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:25.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:25.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:25.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:25.800][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-06-27 12:50:25.803][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:25.804][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:25.805][rule$waitAsNeeded] Wait 0.483097 second(s).
biodb.TRACE[2024-06-27 12:50:26.440][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-27 12:50:26.687][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:26.688][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:26.689][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:26.690][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-27 12:50:27.090][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:27.092][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:27.092][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:27.094][rule$waitAsNeeded] Wait 0.345772 second(s).
biodb.TRACE[2024-06-27 12:50:27.568][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-27 12:50:27.815][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:27.816][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:27.817][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:27.818][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-27 12:50:28.307][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:28.309][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:28.310][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:28.311][rule$waitAsNeeded] Wait 0.256991 second(s).
biodb.TRACE[2024-06-27 12:50:28.719][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-27 12:50:28.969][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:28.970][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:28.971][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:28.972][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-27 12:50:29.456][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:29.457][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:29.458][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:29.459][rule$waitAsNeeded] Wait 0.25949 second(s).
biodb.TRACE[2024-06-27 12:50:29.774][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-27 12:50:29.969][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:29.970][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:29.971][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:29.972][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-27 12:50:30.345][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:30.346][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:30.347][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:30.348][rule$waitAsNeeded] Wait 0.425456 second(s).
biodb.TRACE[2024-06-27 12:50:30.925][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-27 12:50:31.175][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:31.176][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:31.177][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:31.178][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-27 12:50:31.389][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:31.390][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:31.391][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:31.392][rule$waitAsNeeded] Wait 0.532938 second(s).
biodb.TRACE[2024-06-27 12:50:31.961][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-27 12:50:32.197][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:32.198][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:32.200][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:32.201][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-27 12:50:32.685][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:32.687][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:32.688][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:32.689][rule$waitAsNeeded] Wait 0.27187 second(s).
biodb.TRACE[2024-06-27 12:50:33.112][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-27 12:50:33.358][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:33.359][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:33.360][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:33.361][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-27 12:50:33.597][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:33.598][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:33.599][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:33.600][rule$waitAsNeeded] Wait 0.511349 second(s).
biodb.TRACE[2024-06-27 12:50:34.155][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-27 12:50:34.400][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:34.402][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:34.403][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:34.404][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-27 12:50:34.704][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:34.706][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:34.707][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:34.708][rule$waitAsNeeded] Wait 0.447108 second(s).
biodb.TRACE[2024-06-27 12:50:35.305][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-27 12:50:35.549][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:35.550][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:35.551][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:35.552][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-27 12:50:36.086][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-27 12:50:36.087][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:36.088][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:36.089][rule$waitAsNeeded] Wait 0.215575 second(s).
biodb.TRACE[2024-06-27 12:50:36.456][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-27 12:50:36.698][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-27 12:50:36.699][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-27 12:50:36.701][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-27 12:50:36.701][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-27 12:50:36.949][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-06-27 12:50:36.952][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-06-27 12:50:36.954][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-27 12:50:36.956][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-27 12:50:36.957][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-27 12:50:36.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:36.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:36.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:36.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:36.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:36.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:36.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:50:36.970][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:36.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:36.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:36.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:36.974][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:36.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:36.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:36.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:36.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:36.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:36.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:36.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:50:36.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:36.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:36.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:36.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:36.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:36.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:36.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:50:36.992][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:36.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:36.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:36.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:36.995][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:36.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:36.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:36.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:36.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:36.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:37.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:37.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:37.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:37.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:37.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:37.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:37.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:37.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:37.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:37.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:37.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:37.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:37.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:37.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:37.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:37.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:37.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:37.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:37.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:37.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:37.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:37.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:37.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:37.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:37.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:37.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:37.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:37.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:37.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:37.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:37.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:37.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:37.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:37.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:37.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:37.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:37.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:37.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:37.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:37.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:37.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:37.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:50:37.034][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-06-27 12:50:37.035][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-27 12:50:37.036][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-06-27 12:50:37.215][biodb::testThat]
biodb.INFO [2024-06-27 12:50:37.216][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-27 12:50:37.217][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:50:37.218][biodb::testThat]
biodb.INFO [2024-06-27 12:50:37.262][biodb::testThat]
biodb.INFO [2024-06-27 12:50:37.263][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-27 12:50:37.264][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:50:37.265][biodb::testThat]
biodb.INFO [2024-06-27 12:50:37.274][biodb::testThat]
biodb.INFO [2024-06-27 12:50:37.275][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-27 12:50:37.276][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:50:37.277][biodb::testThat]
biodb.DEBUG[2024-06-27 12:50:37.280][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[2024-06-27 12:50:37.284][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:37.285][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:37.286][rule$waitAsNeeded] Wait 0.169435 second(s).
biodb.TRACE[2024-06-27 12:50:37.507][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-06-27 12:50:41.070][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-06-27 12:50:45.827][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:50:45.830][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-06-27 12:50:45.841][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-06-27 12:50:47.138][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:47.139][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:47.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:47.141][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:47.142][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:47.143][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:47.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:47.145][ef$get] fields variable is a list.
biodb.INFO [2024-06-27 12:50:47.147][biodb::testThat]
biodb.INFO [2024-06-27 12:50:47.148][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-27 12:50:47.148][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:50:47.149][biodb::testThat]
biodb.ERROR[2024-06-27 12:50:47.165][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-27 12:50:47.184][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-27 12:50:47.199][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-27 12:50:47.201][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-27 12:50:47.202][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-27 12:50:47.203][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-27 12:50:47.204][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.205][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.207][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-27 12:50:47.219][biodb::testContext]
biodb.INFO [2024-06-27 12:50:47.220][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 12:50:47.221][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-06-27 12:50:47.221][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 12:50:47.222][biodb::testContext]
biodb.INFO [2024-06-27 12:50:47.225][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-27 12:50:47.227][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-27 12:50:47.232][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 12:50:47.233][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-27 12:50:47.234][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-27 12:50:47.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.238][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-27 12:50:47.238][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-27 12:50:47.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.241][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-27 12:50:47.242][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-27 12:50:47.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.245][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-27 12:50:47.246][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-27 12:50:47.247][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-27 12:50:47.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.251][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-27 12:50:47.251][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-27 12:50:47.252][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-27 12:50:47.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.256][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-27 12:50:47.257][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-27 12:50:47.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.260][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-27 12:50:47.261][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-27 12:50:47.261][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-27 12:50:47.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.265][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-27 12:50:47.265][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-27 12:50:47.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.268][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[2024-06-27 12:50:47.268][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-27 12:50:47.269][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-27 12:50:47.270][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-27 12:50:47.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.273][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-27 12:50:47.274][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-27 12:50:47.275][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-27 12:50:47.276][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-27 12:50:47.276][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-27 12:50:47.277][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-27 12:50:47.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.281][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-27 12:50:47.281][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-27 12:50:47.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.284][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-27 12:50:47.285][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-27 12:50:47.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.288][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-27 12:50:47.289][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-27 12:50:47.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.293][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-27 12:50:47.294][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-27 12:50:47.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.297][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-27 12:50:47.298][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-27 12:50:47.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.302][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-27 12:50:47.303][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-27 12:50:47.318][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-27 12:50:47.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.322][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-27 12:50:47.322][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-27 12:50:47.323][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-27 12:50:47.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.327][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-27 12:50:47.328][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.329][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-27 12:50:47.330][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.331][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:50:47.332][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.333][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.334][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.335][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.336][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 12:50:47.336][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:50:47.337][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.338][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-27 12:50:47.339][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:50:47.340][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.341][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.342][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 12:50:47.342][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 12:50:47.342][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 12:50:47.342][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 12:50:47.342][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 12:50:47.343][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:50:47.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:47.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:47.345][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:50:47.346][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:47.347][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:47.348][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.348][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.349][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:50:47.350][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:50:47.351][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.352][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.353][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-27 12:50:47.354][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.355][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 12:50:47.356][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.357][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:50:47.358][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.359][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.360][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.361][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.362][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 12:50:47.362][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:50:47.363][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.364][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-27 12:50:47.365][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:50:47.366][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.367][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.368][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 12:50:47.368][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 12:50:47.368][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 12:50:47.368][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 12:50:47.368][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 12:50:47.369][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:50:47.370][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:47.370][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:47.371][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:50:47.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:47.373][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:47.374][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.375][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.376][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:50:47.376][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:50:47.377][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.378][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.379][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-27 12:50:47.381][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.382][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-27 12:50:47.383][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.383][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:50:47.384][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.385][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.391][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.392][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.393][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 12:50:47.394][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:50:47.395][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.396][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-27 12:50:47.397][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:50:47.398][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.399][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.400][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.401][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:50:47.402][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:47.403][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:47.404][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:50:47.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:47.405][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:47.406][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.426][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.427][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:50:47.428][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:50:47.428][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.429][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.430][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-27 12:50:47.432][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.433][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 12:50:47.434][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.435][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:50:47.435][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.436][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.437][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.438][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.439][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 12:50:47.440][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:50:47.440][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.441][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-27 12:50:47.442][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:50:47.443][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.444][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.445][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.445][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:50:47.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:47.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:47.448][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:50:47.448][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:47.449][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:47.450][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.451][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.452][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:50:47.452][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:50:47.453][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.454][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.455][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 12:50:47.456][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.497][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[2024-06-27 12:50:47.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.501][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[2024-06-27 12:50:47.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.504][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[2024-06-27 12:50:47.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.508][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[2024-06-27 12:50:47.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.512][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[2024-06-27 12:50:47.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.520][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-27 12:50:47.522][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-27 12:50:47.523][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-27 12:50:47.524][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-27 12:50:47.525][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-27 12:50:47.527][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-27 12:50:47.528][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-27 12:50:47.529][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-27 12:50:47.530][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-27 12:50:47.531][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-27 12:50:47.533][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-27 12:50:47.534][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-27 12:50:47.535][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-27 12:50:47.536][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-27 12:50:47.538][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-27 12:50:47.539][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-27 12:50:47.540][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-27 12:50:47.541][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-27 12:50:47.542][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-27 12:50:47.544][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-27 12:50:47.545][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-27 12:50:47.546][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-27 12:50:47.547][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-27 12:50:47.549][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-27 12:50:47.550][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-27 12:50:47.551][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-27 12:50:47.553][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-27 12:50:47.554][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-27 12:50:47.555][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-27 12:50:47.556][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-27 12:50:47.557][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-27 12:50:47.559][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-27 12:50:47.560][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-27 12:50:47.561][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-27 12:50:47.562][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-27 12:50:47.564][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-27 12:50:47.565][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-27 12:50:47.566][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-27 12:50:47.567][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-27 12:50:47.569][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-27 12:50:47.570][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-27 12:50:47.571][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-27 12:50:47.572][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-27 12:50:47.574][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-27 12:50:47.575][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-27 12:50:47.576][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-27 12:50:47.578][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-27 12:50:47.579][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-27 12:50:47.580][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-27 12:50:47.581][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-27 12:50:47.582][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-27 12:50:47.584][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-27 12:50:47.585][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-27 12:50:47.586][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-27 12:50:47.587][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-27 12:50:47.589][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-27 12:50:47.590][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-27 12:50:47.591][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-27 12:50:47.593][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-27 12:50:47.594][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-27 12:50:47.595][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-27 12:50:47.596][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-27 12:50:47.598][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-27 12:50:47.599][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-27 12:50:47.600][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-27 12:50:47.601][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-27 12:50:47.603][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-27 12:50:47.604][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-27 12:50:47.605][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-27 12:50:47.606][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-27 12:50:47.607][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-27 12:50:47.609][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-27 12:50:47.610][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-27 12:50:47.611][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-27 12:50:47.612][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-27 12:50:47.613][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-27 12:50:47.615][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-27 12:50:47.616][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-27 12:50:47.617][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-27 12:50:47.618][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-27 12:50:47.619][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-27 12:50:47.621][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-27 12:50:47.622][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-27 12:50:47.624][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-27 12:50:47.626][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-27 12:50:47.627][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 12:50:47.628][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.629][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.680][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.DEBUG[2024-06-27 12:50:47.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.716][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.DEBUG[2024-06-27 12:50:47.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:47.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:47.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:47.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:47.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:47.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:47.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:47.739][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-27 12:50:47.741][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-27 12:50:47.744][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.746][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.747][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.749][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:50:47.750][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.752][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.753][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.754][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.755][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 12:50:47.756][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:50:47.756][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.757][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-27 12:50:47.758][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:50:47.759][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-27 12:50:47.759][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-27 12:50:47.759][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-27 12:50:47.759][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-27 12:50:47.759][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-27 12:50:47.759][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-27 12:50:47.759][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-27 12:50:47.759][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-27 12:50:47.759][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-27 12:50:47.760][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:47.761][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 12:50:47.761][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 12:50:47.762][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:50:47.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:47.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:47.764][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:50:47.765][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:47.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:47.766][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:50:47.767][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-27 12:50:47.767][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-27 12:50:47.768][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:50:47.769][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:50:47.769][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:47.770][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:47.771][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-27 12:50:47.773][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-27 12:50:47.776][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-27 12:50:47.777][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-27 12:50:47.778][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-27 12:50:47.779][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-27 12:50:47.780][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-27 12:50:47.781][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-27 12:50:47.782][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-27 12:50:47.783][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-27 12:50:47.785][biodb::testThat]
biodb.INFO [2024-06-27 12:50:47.786][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-06-27 12:50:47.787][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:50:47.787][biodb::testThat]
biodb.DEBUG[2024-06-27 12:50:47.791][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[2024-06-27 12:50:47.796][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:47.797][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 12:50:47.798][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-06-27 12:50:48.106][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-06-27 12:50:48.404][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:50:48.406][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-06-27 12:50:48.411][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-06-27 12:50:48.421][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-06-27 12:50:48.424][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:48.425][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:48.426][rule$waitAsNeeded] Wait 0.371945 second(s).
biodb.TRACE[2024-06-27 12:50:48.864][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-06-27 12:50:49.214][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-06-27 12:50:49.519][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:50:49.521][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-06-27 12:50:49.525][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-06-27 12:50:49.537][biodb::testThat]
biodb.INFO [2024-06-27 12:50:49.538][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-06-27 12:50:49.539][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:50:49.540][biodb::testThat]
biodb.INFO [2024-06-27 12:50:49.567][biodb::testThat]
biodb.INFO [2024-06-27 12:50:49.568][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-06-27 12:50:49.569][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:50:49.570][biodb::testThat]
biodb.DEBUG[2024-06-27 12:50:49.573][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-06-27 12:50:49.576][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:49.577][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:49.578][rule$waitAsNeeded] Wait 0.284199 second(s).
biodb.TRACE[2024-06-27 12:50:49.959][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-06-27 12:50:50.105][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-06-27 12:50:50.255][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:50:50.258][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-06-27 12:50:50.263][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-06-27 12:50:50.269][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-06-27 12:50:50.272][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 12:50:50.273][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-06-27 12:50:50.275][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 12:50:50.276][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-06-27 12:50:50.286][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-06-27 12:50:50.290][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:50.291][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:50.293][rule$waitAsNeeded] Wait 0.665746 second(s).
biodb.TRACE[2024-06-27 12:50:51.111][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-06-27 12:50:51.280][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-06-27 12:50:51.429][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:50:51.432][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-06-27 12:50:51.436][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-06-27 12:50:51.444][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-06-27 12:50:51.447][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:51.448][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-27 12:50:51.449][rule$waitAsNeeded] Wait 0.660764 second(s).
biodb.TRACE[2024-06-27 12:50:52.262][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-06-27 12:50:53.168][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-06-27 12:50:54.243][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:50:54.246][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-06-27 12:50:54.251][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-06-27 12:50:54.431][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-06-27 12:50:54.435][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-27 12:50:54.436][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-27 12:50:54.438][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-06-27 12:50:55.362][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-06-27 12:50:56.446][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-27 12:50:56.448][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-06-27 12:50:56.453][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-06-27 12:50:56.668][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-27 12:50:56.670][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-27 12:50:56.671][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-27 12:50:56.672][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-27 12:50:56.673][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:56.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:56.675][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.676][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-27 12:50:56.682][biodb::testContext]
biodb.INFO [2024-06-27 12:50:56.683][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 12:50:56.684][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-06-27 12:50:56.684][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-27 12:50:56.685][biodb::testContext]
biodb.INFO [2024-06-27 12:50:56.688][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-27 12:50:56.689][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-27 12:50:56.695][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 12:50:56.696][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-27 12:50:56.697][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-27 12:50:56.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.700][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-27 12:50:56.701][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-27 12:50:56.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.704][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-27 12:50:56.705][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-27 12:50:56.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.708][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-27 12:50:56.709][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-27 12:50:56.710][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-27 12:50:56.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.713][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-27 12:50:56.714][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-27 12:50:56.715][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-27 12:50:56.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.718][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-27 12:50:56.719][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-27 12:50:56.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.721][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-27 12:50:56.722][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-27 12:50:56.723][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-27 12:50:56.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.726][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-27 12:50:56.727][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-27 12:50:56.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.730][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-27 12:50:56.730][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-27 12:50:56.731][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-27 12:50:56.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.734][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-27 12:50:56.735][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-27 12:50:56.736][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-27 12:50:56.737][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-27 12:50:56.738][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-27 12:50:56.739][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-27 12:50:56.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.742][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-27 12:50:56.743][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-27 12:50:56.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.746][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-27 12:50:56.747][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-27 12:50:56.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.750][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-27 12:50:56.751][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-27 12:50:56.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.753][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-27 12:50:56.754][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-27 12:50:56.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.757][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-27 12:50:56.758][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-27 12:50:56.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.761][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-27 12:50:56.762][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-27 12:50:56.777][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-27 12:50:56.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.780][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[2024-06-27 12:50:56.781][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-27 12:50:56.782][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-27 12:50:56.783][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-27 12:50:56.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.786][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-27 12:50:56.788][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:56.788][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-27 12:50:56.789][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.790][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:50:56.791][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.792][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:50:56.793][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:56.793][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:50:56.794][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 12:50:56.795][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:50:56.796][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.797][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-27 12:50:56.798][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:50:56.798][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.799][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.800][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 12:50:56.800][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 12:50:56.800][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 12:50:56.800][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 12:50:56.800][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 12:50:56.801][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:50:56.802][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:56.803][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:56.804][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:50:56.804][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:56.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:56.806][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:50:56.807][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.808][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:50:56.808][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:50:56.809][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:56.810][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.811][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-27 12:50:56.813][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:56.814][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 12:50:56.814][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.815][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:50:56.816][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.817][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:50:56.818][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:56.818][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:50:56.819][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 12:50:56.820][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:50:56.821][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.822][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-27 12:50:56.822][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:50:56.823][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.824][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.825][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 12:50:56.825][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 12:50:56.825][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-27 12:50:56.825][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-27 12:50:56.825][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-27 12:50:56.826][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:50:56.826][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:56.827][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:56.828][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:50:56.829][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:56.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:56.830][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:50:56.831][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.832][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:50:56.832][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:50:56.833][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:56.834][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.835][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-27 12:50:56.836][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.837][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-27 12:50:56.838][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.839][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:50:56.840][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.842][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:50:56.843][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:56.844][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:50:56.845][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 12:50:56.846][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:50:56.847][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:56.848][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-27 12:50:56.849][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:50:56.850][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.850][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.851][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.852][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:50:56.853][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:56.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:56.855][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:50:56.855][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:56.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:56.857][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:50:56.858][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.859][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:50:56.859][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:50:56.860][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:56.861][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.862][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-27 12:50:56.864][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.865][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-27 12:50:56.866][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.867][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:50:56.867][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.868][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:50:56.869][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:56.870][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:50:56.871][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-27 12:50:56.872][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:50:56.872][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:56.873][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-27 12:50:56.874][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:50:56.875][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.876][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:56.877][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.878][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:50:56.879][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:56.880][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:56.880][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:50:56.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:56.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:56.883][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:50:56.884][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.884][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:50:56.885][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:50:56.886][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:56.887][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:56.888][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 12:50:56.889][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:56.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:56.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:56.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:56.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:56.970][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-27 12:50:56.972][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-27 12:50:56.973][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-27 12:50:56.974][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-27 12:50:56.976][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-27 12:50:56.977][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-27 12:50:56.978][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-27 12:50:56.980][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-27 12:50:56.981][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-27 12:50:56.982][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-27 12:50:56.983][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-27 12:50:56.985][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-27 12:50:56.986][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-27 12:50:56.987][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-27 12:50:56.988][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-27 12:50:56.990][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-27 12:50:56.991][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-27 12:50:56.992][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-27 12:50:56.993][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-27 12:50:56.995][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-27 12:50:56.997][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-27 12:50:56.999][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-27 12:50:57.001][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-27 12:50:57.003][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-27 12:50:57.004][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-27 12:50:57.006][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-27 12:50:57.007][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-27 12:50:57.008][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-27 12:50:57.009][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-27 12:50:57.010][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-27 12:50:57.012][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-27 12:50:57.013][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-27 12:50:57.015][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-27 12:50:57.016][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-27 12:50:57.017][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-27 12:50:57.018][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-27 12:50:57.020][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-27 12:50:57.021][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-27 12:50:57.022][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-27 12:50:57.023][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-27 12:50:57.024][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-27 12:50:57.026][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-27 12:50:57.027][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-27 12:50:57.028][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-27 12:50:57.029][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-27 12:50:57.030][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-27 12:50:57.032][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-27 12:50:57.033][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-27 12:50:57.034][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-27 12:50:57.035][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-27 12:50:57.037][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-27 12:50:57.038][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-27 12:50:57.039][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-27 12:50:57.040][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-27 12:50:57.041][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-27 12:50:57.043][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-27 12:50:57.044][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-27 12:50:57.045][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-27 12:50:57.047][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-27 12:50:57.048][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-27 12:50:57.049][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-27 12:50:57.050][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-27 12:50:57.052][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-27 12:50:57.053][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-27 12:50:57.054][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-27 12:50:57.056][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-27 12:50:57.057][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-27 12:50:57.058][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-27 12:50:57.060][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-27 12:50:57.061][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-27 12:50:57.063][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-27 12:50:57.064][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-27 12:50:57.065][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-27 12:50:57.066][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-27 12:50:57.067][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-27 12:50:57.069][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-27 12:50:57.070][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-27 12:50:57.071][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-27 12:50:57.072][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-27 12:50:57.073][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-27 12:50:57.075][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-27 12:50:57.076][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-27 12:50:57.077][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-27 12:50:57.078][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-27 12:50:57.080][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-27 12:50:57.081][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-27 12:50:57.082][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.084][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-27 12:50:57.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:57.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:57.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:57.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:57.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:57.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-27 12:50:57.189][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-27 12:50:57.191][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-27 12:50:57.193][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:57.194][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-27 12:50:57.195][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:57.196][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-27 12:50:57.197][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:57.197][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-27 12:50:57.198][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:57.199][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-27 12:50:57.200][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-27 12:50:57.201][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-27 12:50:57.201][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:57.202][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-27 12:50:57.203][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-27 12:50:57.204][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-27 12:50:57.204][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-27 12:50:57.204][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-27 12:50:57.204][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-27 12:50:57.204][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-27 12:50:57.204][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-27 12:50:57.204][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-27 12:50:57.204][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-27 12:50:57.204][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-27 12:50:57.205][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-27 12:50:57.206][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-27 12:50:57.206][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-27 12:50:57.206][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-27 12:50:57.207][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:57.208][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:57.209][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-27 12:50:57.209][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-27 12:50:57.210][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-27 12:50:57.211][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-27 12:50:57.212][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-27 12:50:57.212][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-27 12:50:57.213][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-27 12:50:57.213][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-27 12:50:57.214][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-27 12:50:57.215][self$setPropertyValue]
biodb.DEBUG[2024-06-27 12:50:57.216][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-27 12:50:57.217][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-27 12:50:57.221][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-27 12:50:57.221][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-27 12:50:57.223][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-27 12:50:57.224][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-27 12:50:57.225][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-27 12:50:57.226][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-27 12:50:57.227][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-27 12:50:57.228][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-27 12:50:57.229][biodb::testThat]
biodb.INFO [2024-06-27 12:50:57.230][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-06-27 12:50:57.231][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-27 12:50:57.232][biodb::testThat]
biodb.DEBUG[2024-06-27 12:50:57.235][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[2024-06-27 12:50:57.240][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-27 12:50:57.241][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-06-27 12:50:57.242][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-27 12:50:57.307][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-06-27 12:50:58.433][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-06-27 12:50:58.435][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-27 12:50:58.436][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-06-27 12:50:58.438][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-06-27 12:50:58.439][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[2024-06-27 12:50:58.440][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-27 12:50:58.441][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-27 12:50:58.441][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-27 12:50:58.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:58.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:58.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:58.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:58.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:58.450][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:58.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:50:58.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.467][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-27 12:50:58.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-27 12:50:58.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.468][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 12:50:58.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 12:50:58.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.470][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.472][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.473][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.474][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.476][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-27 12:50:58.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.478][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-27 12:50:58.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.479][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.482][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.484][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.486][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.488][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-27 12:50:58.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.490][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-27 12:50:58.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.494][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-27 12:50:58.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.499][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.502][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.503][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.506][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:50:58.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:58.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:58.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:58.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:58.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:58.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:58.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:50:58.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.540][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-27 12:50:58.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-27 12:50:58.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.541][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-27 12:50:58.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-27 12:50:58.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.543][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.544][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.547][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.549][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.551][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-27 12:50:58.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.553][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-27 12:50:58.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.558][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.571][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-27 12:50:58.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.573][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-27 12:50:58.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.575][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.614][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-27 12:50:58.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.616][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.618][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.626][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-27 12:50:58.657][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-06-27 12:50:58.659][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-27 12:50:58.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:58.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:58.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:58.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:58.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:58.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:58.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:50:58.671][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 12:50:58.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 12:50:58.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.673][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 12:50:58.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 12:50:58.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.677][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-27 12:50:58.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-27 12:50:58.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.681][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-27 12:50:58.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-27 12:50:58.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.685][private$selectFields] Fields none
biodb.TRACE[2024-06-27 12:50:58.685][private$selectFields]
biodb.TRACE[2024-06-27 12:50:58.686][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-06-27 12:50:58.687][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 12:50:58.688][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:58.689][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.689][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.691][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.692][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.693][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.695][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.697][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.698][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.700][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.701][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.702][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.703][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.704][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.705][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.707][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.707][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.708][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.710][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.711][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.712][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.713][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.714][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.715][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.716][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.717][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.718][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.720][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.720][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.721][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.723][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.723][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.724][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.726][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.727][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.727][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.729][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.730][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.731][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.732][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.733][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.734][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.735][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.736][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.737][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.738][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.739][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.740][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.741][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.742][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:58.743][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:58.744][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.745][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.746][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.747][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.748][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.749][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.750][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.751][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.752][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.753][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.754][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.755][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.756][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.757][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.759][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.759][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.760][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.762][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.762][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.763][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.765][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.766][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.766][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.768][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.769][private$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[2024-06-27 12:50:58.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.789][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.792][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.795][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.799][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.802][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.805][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.818][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.825][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.828][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.850][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.853][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.856][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.865][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-06-27 12:50:58.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-27 12:50:58.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:58.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:58.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:58.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:58.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:58.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-27 12:50:58.878][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 12:50:58.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 12:50:58.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.882][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-27 12:50:58.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-27 12:50:58.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.885][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-27 12:50:58.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-27 12:50:58.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.888][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-27 12:50:58.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-27 12:50:58.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.891][private$selectFields] Fields none
biodb.TRACE[2024-06-27 12:50:58.892][private$selectFields]
biodb.TRACE[2024-06-27 12:50:58.893][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-06-27 12:50:58.893][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-27 12:50:58.894][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:58.895][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.896][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.897][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.898][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.899][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.900][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.901][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.902][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.903][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.904][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.905][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.906][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.907][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.908][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.909][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.910][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.911][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.912][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.913][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.914][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.915][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.916][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.917][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.918][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.919][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.920][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.921][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.922][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.923][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.924][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.925][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.926][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.927][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.928][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.929][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.930][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.931][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.932][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.933][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.934][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.935][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.936][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.937][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.938][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.939][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.940][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.941][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.942][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.943][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:58.944][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-27 12:50:58.945][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.946][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.947][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.948][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.949][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.950][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.951][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.952][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.953][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.954][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.955][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.956][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.957][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.958][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:58.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.959][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.960][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:58.961][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:58.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.962][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.963][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:58.964][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:58.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.965][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.966][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.967][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:58.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.968][ef$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.969][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-06-27 12:50:58.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-27 12:50:58.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-27 12:50:58.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-27 12:50:58.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.989][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.992][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.995][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-27 12:50:58.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:58.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:58.999][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:58.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:59.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.002][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:59.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:59.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.005][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:59.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-27 12:50:59.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:59.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:59.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:59.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:59.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:59.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-27 12:50:59.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.018][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:59.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:59.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.021][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:59.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:59.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.024][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-27 12:50:59.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-27 12:50:59.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:59.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:59.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:59.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:59.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-27 12:50:59.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-27 12:50:59.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.037][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:59.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:59.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.040][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:59.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:59.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.044][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:59.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-27 12:50:59.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-27 12:50:59.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-27 12:50:59.050][private$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[2024-06-27 12:50:59.051][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-06-27 12:50:59.052][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-06-27 12:50:59.058][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-27 12:50:59.060][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-27 12:50:59.061][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-27 12:50:59.062][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-27 12:50:59.062][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-27 12:50:59.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-27 12:50:59.064][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-27 12:50:59.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-27 12:50:59.065][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-27 12:50:59.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]

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

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

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

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn2.4050.6273.716
LipidmapsStructureEntry0.4080.0150.426