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This page was generated on 2024-06-28 17:39 -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 nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbLipidmaps_1.10.0.tar.gz
StartedAt: 2024-06-26 21:02:19 -0400 (Wed, 26 Jun 2024)
EndedAt: 2024-06-26 21:07:17 -0400 (Wed, 26 Jun 2024)
EllapsedTime: 298.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.10.0’
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘biodbLipidmaps’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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: x86_64-pc-linux-gnu

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 [2024-06-26 21:03:05.460][biodb::testContext]
biodb.INFO [2024-06-26 21:03:05.464][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:03:05.467][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-26 21:03:05.469][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:03:05.471][biodb::testContext]
biodb.INFO [2024-06-26 21:03:05.480][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:03:05.482][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-26 21:03:05.493][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:03:05.495][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-26 21:03:05.497][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-26 21:03:05.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.505][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-26 21:03:05.543][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-26 21:03:05.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.551][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-26 21:03:05.553][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-26 21:03:05.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.559][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-26 21:03:05.561][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-26 21:03:05.563][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-26 21:03:05.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.570][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-26 21:03:05.571][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-26 21:03:05.573][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-26 21:03:05.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.580][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-26 21:03:05.582][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-26 21:03:05.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.588][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-26 21:03:05.590][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-26 21:03:05.592][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-26 21:03:05.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.598][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-26 21:03:05.600][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-26 21:03:05.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.607][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-26 21:03:05.609][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-26 21:03:05.611][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-26 21:03:05.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.618][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:03:05.619][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-26 21:03:05.621][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-26 21:03:05.623][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-26 21:03:05.625][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-26 21:03:05.627][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-26 21:03:05.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.633][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-26 21:03:05.635][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-26 21:03:05.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.642][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-26 21:03:05.644][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-26 21:03:05.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.649][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-26 21:03:05.650][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-26 21:03:05.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.654][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-26 21:03:05.655][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-26 21:03:05.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.659][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-26 21:03:05.660][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-26 21:03:05.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.664][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:03:05.666][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-26 21:03:05.670][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-26 21:03:05.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.674][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-26 21:03:05.676][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-26 21:03:05.677][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-26 21:03:05.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.684][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-26 21:03:05.725][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:05.757][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-26 21:03:05.759][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.760][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:03:05.761][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.762][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:03:05.763][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:05.765][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:03:05.766][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:03:05.767][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:03:05.768][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.769][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-26 21:03:05.770][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:03:05.772][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.773][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.774][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:03:05.774][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:03:05.774][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:03:05.774][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:03:05.774][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:03:05.776][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:03:05.778][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:05.779][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:05.781][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:03:05.782][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:05.784][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:05.785][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:03:05.787][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.789][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:03:05.791][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:03:05.792][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:05.794][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.796][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-26 21:03:05.799][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:05.801][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:03:05.803][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.805][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:03:05.806][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.808][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:03:05.809][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:05.810][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:03:05.812][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:03:05.814][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:03:05.815][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.817][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-26 21:03:05.819][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:03:05.820][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.821][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.822][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:03:05.822][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:03:05.822][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:03:05.822][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:03:05.822][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:03:05.823][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:03:05.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:05.825][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:05.826][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:03:05.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:05.827][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:05.828][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:03:05.829][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.830][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:03:05.831][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:03:05.832][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:05.833][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.834][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-26 21:03:05.836][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.837][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-26 21:03:05.838][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.840][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:03:05.841][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.843][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:03:05.845][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:05.846][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:03:05.849][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:03:05.850][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:03:05.852][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:05.854][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-26 21:03:05.856][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:03:05.858][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.860][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.861][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.863][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:03:05.865][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:05.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:05.868][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:03:05.870][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:05.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:05.873][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:03:05.875][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.877][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:03:05.879][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:03:05.880][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:05.882][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.884][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-26 21:03:05.888][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.889][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:03:05.891][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.892][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:03:05.893][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.894][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:03:05.895][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:05.896][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:03:05.897][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:03:05.898][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:03:05.899][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:05.900][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-26 21:03:05.901][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:03:05.902][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.903][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:05.904][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.906][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:03:05.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:05.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:05.909][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:03:05.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:05.911][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:05.912][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:03:05.914][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.915][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:03:05.916][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:03:05.917][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:05.918][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:05.923][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:03:05.924][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.925][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[2024-06-26 21:03:05.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:05.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:05.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:05.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:05.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:05.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:05.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:05.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:05.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:05.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:05.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:05.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:05.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:05.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:05.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.968][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.DEBUG[2024-06-26 21:03:05.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:05.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:05.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:05.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:05.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:05.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:05.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.987][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.DEBUG[2024-06-26 21:03:05.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:05.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:05.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:05.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:05.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:05.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:05.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:05.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.029][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-26 21:03:06.034][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-26 21:03:06.036][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-26 21:03:06.037][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-26 21:03:06.039][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 21:03:06.041][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-26 21:03:06.042][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-26 21:03:06.043][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-26 21:03:06.045][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-26 21:03:06.046][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-26 21:03:06.048][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 21:03:06.049][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-26 21:03:06.051][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-26 21:03:06.052][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-26 21:03:06.054][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-26 21:03:06.055][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 21:03:06.056][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-26 21:03:06.058][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-26 21:03:06.059][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 21:03:06.061][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-26 21:03:06.062][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-26 21:03:06.063][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-26 21:03:06.065][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-26 21:03:06.066][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-26 21:03:06.068][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-26 21:03:06.069][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-26 21:03:06.070][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-26 21:03:06.072][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-26 21:03:06.073][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-26 21:03:06.074][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-26 21:03:06.076][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-26 21:03:06.077][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-26 21:03:06.078][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-26 21:03:06.080][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-26 21:03:06.081][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-26 21:03:06.083][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-26 21:03:06.084][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-26 21:03:06.092][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-26 21:03:06.094][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-26 21:03:06.095][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-26 21:03:06.097][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-26 21:03:06.099][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-26 21:03:06.101][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-26 21:03:06.103][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-26 21:03:06.104][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-26 21:03:06.106][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-26 21:03:06.108][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-26 21:03:06.110][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-26 21:03:06.111][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-26 21:03:06.113][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-26 21:03:06.115][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-26 21:03:06.116][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-26 21:03:06.118][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-26 21:03:06.120][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-26 21:03:06.121][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-26 21:03:06.123][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-26 21:03:06.124][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-26 21:03:06.126][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-26 21:03:06.127][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-26 21:03:06.129][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-26 21:03:06.130][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-26 21:03:06.132][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-26 21:03:06.133][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-26 21:03:06.134][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-26 21:03:06.136][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-26 21:03:06.137][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-26 21:03:06.139][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 21:03:06.140][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 21:03:06.141][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-26 21:03:06.143][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-26 21:03:06.144][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-26 21:03:06.145][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-26 21:03:06.147][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-26 21:03:06.148][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-26 21:03:06.150][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-26 21:03:06.151][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-26 21:03:06.152][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-26 21:03:06.154][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-26 21:03:06.156][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-26 21:03:06.158][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-26 21:03:06.159][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-26 21:03:06.160][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-26 21:03:06.162][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-26 21:03:06.169][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-26 21:03:06.170][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:03:06.174][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:03:06.175][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.178][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.237][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[2024-06-26 21:03:06.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.244][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[2024-06-26 21:03:06.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.272][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[2024-06-26 21:03:06.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.293][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[2024-06-26 21:03:06.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:03:06.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:06.319][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-26 21:03:06.330][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 21:03:06.332][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:06.334][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-26 21:03:06.335][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:06.336][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:03:06.337][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:06.338][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:03:06.339][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:06.340][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:03:06.341][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:03:06.342][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:03:06.343][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:06.344][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-26 21:03:06.345][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:03:06.346][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-26 21:03:06.346][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-26 21:03:06.346][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-26 21:03:06.346][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-26 21:03:06.346][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-26 21:03:06.346][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-26 21:03:06.346][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-26 21:03:06.346][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-26 21:03:06.346][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-26 21:03:06.347][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-26 21:03:06.348][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:03:06.348][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:03:06.349][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:03:06.350][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:06.351][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:06.352][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:03:06.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:03:06.354][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:03:06.354][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:03:06.356][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 21:03:06.356][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-26 21:03:06.357][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:03:06.358][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:03:06.359][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-26 21:03:06.360][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:03:06.366][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-26 21:03:06.368][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 21:03:06.401][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 21:03:06.403][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-26 21:03:06.407][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 21:03:06.412][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-26 21:03:06.417][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-26 21:03:06.418][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-26 21:03:06.420][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-26 21:03:06.421][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-26 21:03:06.431][biodb::testThat]
biodb.INFO [2024-06-26 21:03:06.433][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-26 21:03:06.434][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:06.435][biodb::testThat]
biodb.TRACE[2024-06-26 21:03:06.439][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-06-26 21:03:06.441][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:03:06.445][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-26 21:03:06.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:06.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:06.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:06.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:06.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:06.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:06.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:03:06.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:03:06.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:03:06.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.517][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 21:03:06.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 21:03:06.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.521][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:03:06.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:03:06.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.526][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:06.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:06.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.557][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:06.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:06.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.561][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:06.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:06.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.566][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:06.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:06.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.570][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 21:03:06.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:06.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.575][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 21:03:06.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:06.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.580][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:06.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:06.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.585][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:06.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:06.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:06.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:06.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:06.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:06.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.599][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 21:03:06.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:06.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.604][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-26 21:03:06.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:06.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:06.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:06.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.612][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:06.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:06.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.617][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 21:03:06.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:06.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:06.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:06.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.661][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:06.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:06.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:06.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:06.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:06.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:06.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:06.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:06.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.736][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.741][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.750][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:03:06.790][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-26 21:03:06.793][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:03:06.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:03:06.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.797][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:03:06.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:03:06.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.803][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-26 21:03:06.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-26 21:03:06.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.810][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-26 21:03:06.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-26 21:03:06.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.871][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.913][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.917][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.925][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:06.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.969][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.971][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.974][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:06.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:06.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:06.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:06.999][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.007][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.014][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.021][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.022][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.041][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.082][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.089][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.096][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.097][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.101][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.102][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.120][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:07.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:07.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.128][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:07.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:07.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:07.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:07.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.141][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:07.142][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:07.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.145][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.147][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:07.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:07.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.182][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.183][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.185][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.204][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.209][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.213][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.217][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.219][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.221][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.222][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.242][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:07.245][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:07.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.248][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.255][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.257][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.259][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.267][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:07.270][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:07.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.273][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.279][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.281][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.285][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.293][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.295][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.298][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.305][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.307][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.310][ef$get] fields variable is a list.
biodb.INFO [2024-06-26 21:03:07.324][biodb::testThat]
biodb.INFO [2024-06-26 21:03:07.325][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-26 21:03:07.327][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:07.329][biodb::testThat]
biodb.DEBUG[2024-06-26 21:03:07.348][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-06-26 21:03:07.356][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:03:07.361][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-06-26 21:03:07.362][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:03:07.363][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-06-26 21:03:07.365][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:03:07.388][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:03:07.389][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-26 21:03:07.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:07.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:07.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:07.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:07.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:07.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:07.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:03:07.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:07.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:07.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:07.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:07.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:03:07.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:03:07.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:03:07.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:03:07.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.438][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 21:03:07.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 21:03:07.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.442][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:03:07.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:03:07.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.446][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.450][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:07.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.454][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.458][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:07.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.462][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 21:03:07.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.466][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 21:03:07.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:07.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:07.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:07.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.475][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:07.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:07.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.487][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 21:03:07.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.491][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-26 21:03:07.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.504][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 21:03:07.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.521][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.526][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.530][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:07.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:07.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.535][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:07.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:07.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:07.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:07.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.544][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:07.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:07.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:07.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:07.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:07.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:07.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:07.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:07.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:07.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:07.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:07.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:07.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:07.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:07.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:03:07.578][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-06-26 21:03:07.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-26 21:03:07.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-26 21:03:07.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-26 21:03:07.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-26 21:03:07.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-26 21:03:07.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-26 21:03:07.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 21:03:07.600][biodb::testThat]
biodb.INFO [2024-06-26 21:03:07.601][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-26 21:03:07.602][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:07.603][biodb::testThat]
biodb.TRACE[2024-06-26 21:03:07.606][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.607][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.609][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:03:07.610][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-06-26 21:03:07.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:07.650][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:07.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:07.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:07.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:03:07.657][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-26 21:03:07.663][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[2024-06-26 21:03:07.685][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:03:07.686][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:03:07.688][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-06-26 21:03:08.460][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-06-26 21:03:09.096][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:03:09.100][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-06-26 21:03:09.132][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-06-26 21:03:09.136][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-06-26 21:03:09.154][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:09.156][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:09.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:09.159][ef$get] fields variable is a list.
biodb.INFO [2024-06-26 21:03:09.165][biodb::testThat]
biodb.INFO [2024-06-26 21:03:09.166][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-26 21:03:09.168][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:09.169][biodb::testThat]
biodb.TRACE[2024-06-26 21:03:09.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:09.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:09.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:09.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:09.247][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:09.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:09.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:09.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:09.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:09.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:09.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:09.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:03:09.414][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-26 21:03:09.418][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:03:09.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-26 21:03:09.438][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:03:09.440][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-06-26 21:03:09.468][biodb::testThat]
biodb.INFO [2024-06-26 21:03:09.469][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-26 21:03:09.471][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:09.472][biodb::testThat]
biodb.TRACE[2024-06-26 21:03:09.502][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:03:09.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:03:09.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:09.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:09.508][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:03:09.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:03:09.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:09.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:09.515][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-26 21:03:09.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-26 21:03:09.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:09.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:09.521][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-26 21:03:09.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-26 21:03:09.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:09.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:09.575][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:03:09.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:03:09.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:09.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:09.580][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:03:09.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:03:09.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:09.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:09.585][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-26 21:03:09.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-26 21:03:09.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:09.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:09.589][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-26 21:03:09.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-26 21:03:09.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:09.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 21:03:09.600][biodb::testThat]
biodb.INFO [2024-06-26 21:03:09.601][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-26 21:03:09.602][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:09.603][biodb::testThat]
biodb.INFO [2024-06-26 21:03:09.614][biodb::testThat]
biodb.INFO [2024-06-26 21:03:09.616][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-26 21:03:09.617][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:09.618][biodb::testThat]
biodb.INFO [2024-06-26 21:03:09.628][biodb::testThat]
biodb.INFO [2024-06-26 21:03:09.631][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-26 21:03:09.632][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:09.634][biodb::testThat]
biodb.DEBUG[2024-06-26 21:03:09.641][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-06-26 21:03:10.413][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-06-26 21:03:10.837][biodb::testThat]
biodb.INFO [2024-06-26 21:03:10.839][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-26 21:03:10.840][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:10.840][biodb::testThat]
biodb.TRACE[2024-06-26 21:03:10.848][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:10.849][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:10.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:10.851][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:10.852][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:10.853][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:10.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:10.854][ef$get] fields variable is a list.
biodb.INFO [2024-06-26 21:03:10.856][biodb::testThat]
biodb.INFO [2024-06-26 21:03:10.857][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-26 21:03:10.858][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:10.859][biodb::testThat]
biodb.TRACE[2024-06-26 21:03:10.870][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:10.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:10.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:10.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:10.884][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:10.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:10.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:10.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:10.888][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:10.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:10.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:10.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:03:10.977][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-26 21:03:10.982][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:03:10.984][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-26 21:03:10.985][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:03:10.987][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-06-26 21:03:11.049][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-06-26 21:03:11.053][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:03:11.054][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-06-26 21:03:11.056][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:03:11.057][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-06-26 21:03:11.071][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-26 21:03:11.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-26 21:03:11.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:11.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:11.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:03:11.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:03:11.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:11.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:11.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:11.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:11.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:11.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:11.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:11.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:11.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:11.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:11.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:11.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:11.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:11.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:11.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:11.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:11.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:11.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:11.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:11.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:11.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:11.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:03:11.123][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-06-26 21:03:11.138][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:03:11.139][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:03:11.154][private$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[2024-06-26 21:03:15.274][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[2024-06-26 21:03:25.286][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:03:25.292][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-06-26 21:03:25.316][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-06-26 21:03:26.965][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[2024-06-26 21:03:26.973][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:03:26.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:03:26.980][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-06-26 21:03:27.654][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-06-26 21:03:28.320][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:03:28.324][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-06-26 21:03:28.331][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-06-26 21:03:28.368][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-06-26 21:03:28.375][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:03:28.378][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:03:28.382][private$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[2024-06-26 21:03:29.106][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[2024-06-26 21:03:29.732][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:03:29.737][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-06-26 21:03:29.746][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-06-26 21:03:29.781][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-26 21:03:29.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-26 21:03:29.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:29.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 21:03:29.803][biodb::testThat]
biodb.INFO [2024-06-26 21:03:29.805][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-26 21:03:29.807][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:29.809][biodb::testThat]
biodb.TRACE[2024-06-26 21:03:29.817][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-26 21:03:29.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-26 21:03:29.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:29.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:29.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:03:29.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:03:29.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:29.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:29.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:29.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:29.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:29.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:29.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:29.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:29.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:29.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:29.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:29.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:29.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:29.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:29.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:29.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:29.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:29.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:03:29.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:29.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:29.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:29.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:29.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:29.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:29.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:29.889][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[2024-06-26 21:03:29.894][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:03:29.896][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:03:29.899][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-06-26 21:03:33.858][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-06-26 21:03:43.606][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:03:43.609][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-06-26 21:03:43.620][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-06-26 21:03:44.787][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-06-26 21:03:44.834][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-26 21:03:44.836][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-06-26 21:03:44.838][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-26 21:03:44.839][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:03:44.840][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:03:44.841][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 21:03:44.842][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:03:44.843][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:03:44.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:44.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:44.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:44.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:44.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:44.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:44.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:44.867][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-06-26 21:03:44.870][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:03:44.871][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:03:44.872][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-06-26 21:03:45.532][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-06-26 21:03:46.154][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:03:46.157][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-06-26 21:03:46.161][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-06-26 21:03:46.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:46.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:46.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:46.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:46.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:46.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:46.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:46.177][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-06-26 21:03:46.180][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:03:46.181][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:03:46.182][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-06-26 21:03:46.791][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-06-26 21:03:47.427][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:03:47.430][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-06-26 21:03:47.434][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-06-26 21:03:47.437][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-06-26 21:03:47.439][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:03:47.441][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-26 21:03:47.442][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-26 21:03:47.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:47.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:47.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:47.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:47.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:47.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:47.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:03:47.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:03:47.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:03:47.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:03:47.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:03:47.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.491][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 21:03:47.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 21:03:47.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.495][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:03:47.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:03:47.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.499][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:47.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:47.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.504][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:47.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:47.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.508][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:47.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:47.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.512][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:47.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:47.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.517][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 21:03:47.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:47.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.521][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 21:03:47.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:47.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:47.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:47.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:47.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:47.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:47.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:47.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.542][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 21:03:47.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.546][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-26 21:03:47.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:47.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:47.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.558][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 21:03:47.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.562][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.566][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.574][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:03:47.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:47.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:47.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:47.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:47.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:47.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:47.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:03:47.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:03:47.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:03:47.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.619][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 21:03:47.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 21:03:47.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.623][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:03:47.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:03:47.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.628][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:47.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:47.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.632][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:47.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:03:47.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.637][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:47.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:47.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.641][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:47.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:03:47.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.645][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 21:03:47.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:47.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.649][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 21:03:47.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:47.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.654][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:47.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:47.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.658][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:03:47.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:03:47.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.663][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:47.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:47.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.671][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 21:03:47.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.676][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-26 21:03:47.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:47.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:03:47.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.727][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 21:03:47.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:03:47.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.732][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.736][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.744][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:03:47.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:03:47.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:03:47.786][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-06-26 21:03:47.796][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 21:03:47.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:47.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:47.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:47.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:47.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:47.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:47.807][FUN] Functions in observer BiodbConfig: [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[2024-06-26 21:03:47.809][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.813][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.817][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:03:47.818][private$selectFields]
biodb.TRACE[2024-06-26 21:03:47.819][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:03:47.820][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:03:47.821][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:03:47.822][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.823][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.825][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.826][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.827][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.829][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.830][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:03:47.830][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:03:47.831][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.832][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.834][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.835][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 21:03:47.836][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.840][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.844][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.856][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-26 21:03:47.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:47.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:47.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:47.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:47.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:47.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:47.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:03:47.867][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.871][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.874][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:03:47.875][private$selectFields]
biodb.TRACE[2024-06-26 21:03:47.876][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:03:47.877][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:03:47.878][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:03:47.879][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.880][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.882][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.883][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.884][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.885][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.886][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:03:47.887][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:03:47.888][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.889][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.891][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.892][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 21:03:47.893][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.897][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.900][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.905][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-26 21:03:47.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:47.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:47.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:47.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:47.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:47.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:47.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:03:47.915][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.919][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.923][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:03:47.923][private$selectFields]
biodb.TRACE[2024-06-26 21:03:47.924][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:03:47.925][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:03:47.926][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:03:47.927][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.928][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.930][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.931][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.932][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.934][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.934][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:03:47.935][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:03:47.936][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.937][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.939][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.940][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 21:03:47.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.945][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.948][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:03:47.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.952][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-26 21:03:47.953][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 21:03:47.954][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-26 21:03:47.963][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-26 21:03:47.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-26 21:03:47.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 21:03:47.970][biodb::testThat]
biodb.INFO [2024-06-26 21:03:47.971][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-26 21:03:47.972][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:03:47.972][biodb::testThat]
biodb.TRACE[2024-06-26 21:03:47.975][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-26 21:03:47.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-26 21:03:47.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:03:47.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:03:47.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:47.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:47.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:47.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:47.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:47.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:47.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:03:47.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:47.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:03:47.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:03:47.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:03:48.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:03:48.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:03:48.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:03:48.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:03:48.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:03:48.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:03:48.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:03:48.070][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[2024-06-26 21:03:48.073][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:03:48.074][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:03:48.076][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-06-26 21:03:52.317][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-06-26 21:04:02.037][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:04:02.040][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-06-26 21:04:02.052][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-06-26 21:04:03.152][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 21:04:03.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:03.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:03.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:03.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:03.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:03.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:03.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:04:03.193][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.197][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.218][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:03.219][private$selectFields]
biodb.TRACE[2024-06-26 21:04:03.220][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:04:03.221][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:04:03.222][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:03.223][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.224][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.226][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.227][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.228][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.229][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.230][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:03.240][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:03.241][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.241][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.243][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.244][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 21:04:03.245][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.249][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.253][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.257][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-26 21:04:03.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:03.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:03.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:03.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:03.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:03.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:03.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:04:03.267][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.271][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.275][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:03.276][private$selectFields]
biodb.TRACE[2024-06-26 21:04:03.276][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:04:03.277][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:04:03.278][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:03.279][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.280][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.282][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.283][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.284][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.286][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.287][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:03.288][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:03.288][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.289][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.291][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.292][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 21:04:03.293][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.297][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.301][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.305][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-26 21:04:03.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:03.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:03.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:03.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:03.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:03.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:03.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:04:03.315][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.319][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.323][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:03.324][private$selectFields]
biodb.TRACE[2024-06-26 21:04:03.325][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:04:03.326][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:04:03.326][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:03.327][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.328][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.330][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.331][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.332][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.334][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.335][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:03.336][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:03.337][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.338][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.339][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.340][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 21:04:03.341][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.345][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.349][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:03.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.353][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-26 21:04:03.354][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 21:04:03.355][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-26 21:04:03.362][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-26 21:04:03.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-26 21:04:03.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 21:04:03.369][biodb::testThat]
biodb.INFO [2024-06-26 21:04:03.370][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-26 21:04:03.370][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:04:03.371][biodb::testThat]
biodb.TRACE[2024-06-26 21:04:03.374][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-26 21:04:03.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-26 21:04:03.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-26 21:04:03.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-26 21:04:03.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:04:03.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:04:03.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:04:03.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:04:03.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:04:03.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:04:03.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:03.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:04:03.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:04:03.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:03.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:04:03.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:03.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:03.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:03.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:03.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:03.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:03.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:04:03.411][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-06-26 21:04:03.414][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:04:03.415][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-06-26 21:04:03.417][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:04:03.460][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-06-26 21:04:04.589][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 21:04:04.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:04.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:04.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:04.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:04.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:04.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:04.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:04:04.601][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.604][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.608][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:04.609][private$selectFields]
biodb.TRACE[2024-06-26 21:04:04.610][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:04:04.611][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:04:04.612][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:04.612][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.613][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.615][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.616][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.617][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.619][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.620][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:04.621][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:04.622][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.623][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.624][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.625][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 21:04:04.626][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.630][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.634][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.638][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-06-26 21:04:04.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:04.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:04.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:04.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:04.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:04.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:04.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:04:04.649][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.652][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.656][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:04.657][private$selectFields]
biodb.TRACE[2024-06-26 21:04:04.658][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:04:04.659][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:04:04.660][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:04.661][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.662][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.663][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.664][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.665][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.667][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.668][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:04.669][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:04.670][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.671][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.673][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.673][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 21:04:04.674][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.678][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.682][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.686][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-06-26 21:04:04.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:04.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:04.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:04.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:04.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:04.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:04.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:04:04.696][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.700][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.703][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:04.704][private$selectFields]
biodb.TRACE[2024-06-26 21:04:04.705][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-26 21:04:04.706][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:04:04.707][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:04.708][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.709][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.710][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.711][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.712][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.714][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.715][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:04.716][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:04:04.717][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.718][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.719][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.720][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-06-26 21:04:04.721][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.725][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.729][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:04.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:04.733][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-06-26 21:04:04.733][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 21:04:04.734][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-26 21:04:04.750][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-26 21:04:04.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-26 21:04:04.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:04.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-26 21:04:04.756][biodb::testThat]
biodb.INFO [2024-06-26 21:04:04.757][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-26 21:04:04.758][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:04:04.759][biodb::testThat]
biodb.DEBUG[2024-06-26 21:04:04.761][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-26 21:04:04.762][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-26 21:04:04.763][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-26 21:04:04.764][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-26 21:04:04.765][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:04:04.766][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:04:04.767][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 21:04:04.768][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:04:04.769][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:04:04.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:04.783][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:04.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:04.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:04.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:04.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:04.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:04:04.791][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-06-26 21:04:04.794][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:04.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:04.796][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 21:04:05.410][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:05.411][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:05.413][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:05.414][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 21:04:06.107][private$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[2024-06-26 21:04:06.109][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:06.109][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:06.111][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 21:04:06.730][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:06.732][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:06.733][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:06.734][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 21:04:07.483][private$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[2024-06-26 21:04:07.484][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:07.485][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:07.487][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 21:04:08.120][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:08.122][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:08.125][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:08.127][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 21:04:08.821][private$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[2024-06-26 21:04:08.824][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:08.826][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:08.829][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 21:04:09.445][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:09.446][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:09.448][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:09.449][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 21:04:10.248][private$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[2024-06-26 21:04:10.250][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:10.251][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:10.253][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 21:04:10.879][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:10.881][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:10.883][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:10.886][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 21:04:11.678][private$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[2024-06-26 21:04:11.680][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:11.683][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:11.686][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 21:04:12.342][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:12.344][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:12.346][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:12.347][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 21:04:13.039][private$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[2024-06-26 21:04:13.040][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:13.041][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:13.043][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 21:04:13.631][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:13.632][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:13.633][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:13.635][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 21:04:14.381][private$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[2024-06-26 21:04:14.383][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:14.384][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:14.385][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 21:04:14.954][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:14.956][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:14.959][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:14.962][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 21:04:15.708][private$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[2024-06-26 21:04:15.710][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:15.711][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:15.712][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 21:04:16.285][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:16.286][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:16.287][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:16.289][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 21:04:17.034][private$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[2024-06-26 21:04:17.036][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:17.037][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:17.038][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-06-26 21:04:17.602][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:17.603][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:17.604][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:17.606][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-06-26 21:04:18.358][private$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[2024-06-26 21:04:18.370][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-06-26 21:04:18.375][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:04:18.380][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-06-26 21:04:18.384][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-26 21:04:18.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:18.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:18.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:18.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:18.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:18.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:18.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:04:18.427][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:18.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:18.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:18.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:18.434][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:18.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:18.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:18.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:18.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:18.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:18.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:18.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:18.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:18.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:18.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:18.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:18.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:18.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:18.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:18.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:18.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:18.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:18.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:18.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:18.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:18.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:18.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:18.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:18.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:18.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:18.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:18.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:04:18.570][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-06-26 21:04:18.571][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-26 21:04:18.580][biodb::testThat]
biodb.INFO [2024-06-26 21:04:18.582][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-26 21:04:18.583][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:04:18.584][biodb::testThat]
biodb.DEBUG[2024-06-26 21:04:18.594][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-06-26 21:04:18.595][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-06-26 21:04:18.597][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-26 21:04:18.599][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-06-26 21:04:18.600][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-26 21:04:18.602][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-26 21:04:18.603][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:04:18.605][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 21:04:18.606][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-26 21:04:18.607][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-26 21:04:18.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:18.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:18.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:18.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:18.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:18.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:18.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:04:18.625][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-06-26 21:04:18.629][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:18.630][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:18.632][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 21:04:19.183][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:19.184][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:19.186][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[2024-06-26 21:04:19.187][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 21:04:19.974][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 21:04:19.977][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:19.980][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:19.984][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 21:04:20.581][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:20.583][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:20.586][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[2024-06-26 21:04:20.589][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 21:04:21.380][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 21:04:21.382][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:21.383][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:21.385][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 21:04:21.925][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:21.927][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:21.929][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[2024-06-26 21:04:21.930][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 21:04:22.722][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 21:04:22.724][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:22.725][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:22.727][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 21:04:23.324][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:23.327][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:23.330][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[2024-06-26 21:04:23.333][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 21:04:24.041][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 21:04:24.049][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:24.052][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:24.058][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 21:04:24.600][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:24.602][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:24.605][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[2024-06-26 21:04:24.608][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 21:04:25.402][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 21:04:25.403][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:25.405][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:25.406][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 21:04:26.000][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:26.002][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:26.004][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[2024-06-26 21:04:26.007][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 21:04:26.799][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 21:04:26.803][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:26.806][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:26.809][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 21:04:27.418][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:27.420][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:27.421][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[2024-06-26 21:04:27.422][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 21:04:28.212][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 21:04:28.214][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:28.215][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:28.217][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 21:04:28.775][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:28.777][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:28.780][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[2024-06-26 21:04:28.783][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 21:04:29.575][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 21:04:29.576][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:29.577][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:29.579][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 21:04:30.156][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:30.158][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:30.160][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[2024-06-26 21:04:30.162][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 21:04:30.932][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 21:04:30.935][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:30.936][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:30.938][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-06-26 21:04:31.502][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:31.503][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:31.505][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[2024-06-26 21:04:31.506][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-06-26 21:04:32.256][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-06-26 21:04:32.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:32.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:32.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:32.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:32.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:32.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:32.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:04:32.278][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-06-26 21:04:32.283][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:32.285][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:32.287][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 21:04:32.888][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:32.889][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:32.891][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:32.892][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 21:04:33.637][private$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[2024-06-26 21:04:33.639][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:33.640][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:33.641][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 21:04:34.205][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:34.206][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:34.207][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:34.208][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 21:04:34.955][private$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[2024-06-26 21:04:34.957][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:34.958][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:34.959][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 21:04:35.519][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:35.521][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:35.522][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:35.523][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 21:04:36.320][private$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[2024-06-26 21:04:36.322][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:36.324][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:36.326][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 21:04:36.905][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:36.907][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:36.908][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:36.909][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 21:04:37.660][private$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[2024-06-26 21:04:37.662][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:37.664][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:37.667][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 21:04:38.255][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:38.256][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:38.257][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:38.258][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 21:04:38.950][private$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[2024-06-26 21:04:38.952][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:38.953][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:38.954][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 21:04:39.527][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:39.531][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:39.533][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:39.534][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 21:04:40.318][private$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[2024-06-26 21:04:40.320][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:40.321][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:40.323][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 21:04:40.903][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:40.904][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:40.906][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:40.907][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 21:04:41.654][private$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[2024-06-26 21:04:41.655][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:41.657][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:41.659][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 21:04:42.219][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:42.221][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:42.222][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:42.223][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 21:04:42.971][private$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[2024-06-26 21:04:42.973][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:42.974][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:42.975][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 21:04:43.526][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:43.527][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:43.529][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:43.530][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 21:04:44.285][private$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[2024-06-26 21:04:44.288][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:44.290][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:44.294][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-06-26 21:04:44.805][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-06-26 21:04:44.807][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-26 21:04:44.808][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-26 21:04:44.809][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-06-26 21:04:45.558][private$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[2024-06-26 21:04:45.562][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-06-26 21:04:45.564][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-26 21:04:45.566][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-26 21:04:45.567][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-26 21:04:45.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:45.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:45.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:45.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:45.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:45.582][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:45.583][FUN] Functions in observer BiodbConfig: [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[2024-06-26 21:04:45.585][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:45.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:45.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.590][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:45.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:45.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:45.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:45.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:04:45.598][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:04:45.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:04:45.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:04:45.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:04:45.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:04:45.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:04:45.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:04:45.609][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:45.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:45.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.613][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:45.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:04:45.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:45.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:45.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:45.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:45.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:45.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:45.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:45.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:45.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:45.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:45.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:45.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:45.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:45.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:45.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:45.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:45.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:45.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:45.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:45.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:45.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:04:45.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:04:45.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:04:45.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:04:45.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:04:45.664][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-06-26 21:04:45.665][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-26 21:04:45.667][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-06-26 21:04:45.893][biodb::testThat]
biodb.INFO [2024-06-26 21:04:45.894][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-26 21:04:45.895][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:04:45.896][biodb::testThat]
biodb.INFO [2024-06-26 21:04:45.940][biodb::testThat]
biodb.INFO [2024-06-26 21:04:45.942][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-26 21:04:45.943][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:04:45.944][biodb::testThat]
biodb.INFO [2024-06-26 21:04:45.951][biodb::testThat]
biodb.INFO [2024-06-26 21:04:45.952][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-26 21:04:45.953][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:04:45.954][biodb::testThat]
biodb.DEBUG[2024-06-26 21:04:45.958][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[2024-06-26 21:04:45.961][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:04:45.962][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:04:45.964][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-06-26 21:04:49.783][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-06-26 21:04:59.834][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:04:59.837][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-06-26 21:04:59.849][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-06-26 21:05:00.805][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:00.806][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:00.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:00.808][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:00.809][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:00.811][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:00.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:00.813][ef$get] fields variable is a list.
biodb.INFO [2024-06-26 21:05:00.815][biodb::testThat]
biodb.INFO [2024-06-26 21:05:00.816][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-26 21:05:00.817][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:05:00.818][biodb::testThat]
biodb.ERROR[2024-06-26 21:05:00.834][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-26 21:05:00.853][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-26 21:05:00.867][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-26 21:05:00.868][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-26 21:05:00.870][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-26 21:05:00.871][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-26 21:05:00.871][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:00.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:00.873][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:00.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:00.875][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-26 21:05:00.886][biodb::testContext]
biodb.INFO [2024-06-26 21:05:00.888][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:05:00.889][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-06-26 21:05:00.889][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:05:00.890][biodb::testContext]
biodb.INFO [2024-06-26 21:05:00.893][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:05:00.894][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-26 21:05:00.899][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:05:00.900][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-26 21:05:00.901][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-26 21:05:00.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.905][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-26 21:05:00.906][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-26 21:05:00.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.909][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-26 21:05:00.910][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-26 21:05:00.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.914][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-26 21:05:00.915][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-26 21:05:00.916][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-26 21:05:00.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.920][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-26 21:05:00.921][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-26 21:05:00.922][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-26 21:05:00.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.925][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[2024-06-26 21:05:00.926][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-26 21:05:00.927][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-26 21:05:00.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.930][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-26 21:05:00.931][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-26 21:05:00.933][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-26 21:05:00.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.935][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[2024-06-26 21:05:00.936][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-26 21:05:00.937][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-26 21:05:00.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.941][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-26 21:05:00.942][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-26 21:05:00.943][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-26 21:05:00.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.946][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:05:00.948][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-26 21:05:00.949][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-26 21:05:00.950][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-26 21:05:00.951][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-26 21:05:00.952][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-26 21:05:00.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.956][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-26 21:05:00.957][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-26 21:05:00.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.961][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-26 21:05:00.962][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-26 21:05:00.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.966][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-26 21:05:00.967][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-26 21:05:00.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.970][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-26 21:05:00.972][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-26 21:05:00.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.975][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-26 21:05:00.976][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-26 21:05:00.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.980][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:05:00.981][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-26 21:05:00.984][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-26 21:05:00.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.988][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-26 21:05:00.989][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-26 21:05:00.990][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-26 21:05:00.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:00.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:00.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:00.994][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-26 21:05:00.996][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:00.997][self$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[2024-06-26 21:05:00.998][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:00.999][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:05:01.000][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.001][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.002][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.003][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.004][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:05:01.005][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:05:01.007][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.007][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-26 21:05:01.008][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:05:01.009][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.010][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.011][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:05:01.011][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:05:01.011][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:05:01.011][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:05:01.011][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:05:01.013][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:05:01.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:01.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:01.015][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:05:01.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:01.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:01.018][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.019][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.020][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:05:01.021][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:05:01.022][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.023][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.024][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-26 21:05:01.026][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.027][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:05:01.028][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.029][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:05:01.030][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.031][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.032][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.033][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.034][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:05:01.035][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:05:01.036][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.038][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-26 21:05:01.039][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:05:01.040][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.041][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.042][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:05:01.042][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:05:01.042][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:05:01.042][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:05:01.042][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:05:01.043][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:05:01.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:01.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:01.046][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:05:01.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:01.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:01.048][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.049][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.050][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:05:01.051][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:05:01.052][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.053][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.054][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-26 21:05:01.056][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.057][self$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[2024-06-26 21:05:01.058][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.059][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:05:01.060][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.061][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.062][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.063][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.064][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:05:01.065][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:05:01.066][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.067][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-26 21:05:01.069][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:05:01.070][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.071][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.072][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.073][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:05:01.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:01.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:01.076][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:05:01.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:01.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:01.079][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.080][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.081][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:05:01.081][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:05:01.082][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.083][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.085][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-26 21:05:01.086][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.087][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:05:01.088][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.089][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:05:01.090][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.091][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.092][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.093][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.094][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:05:01.096][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:05:01.097][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.098][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-26 21:05:01.099][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:05:01.100][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.101][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.102][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.103][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:05:01.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:01.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:01.106][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:05:01.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:01.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:01.108][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.109][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.110][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:05:01.111][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:05:01.112][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.113][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.115][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:05:01.115][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.116][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[2024-06-26 21:05:01.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.121][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[2024-06-26 21:05:01.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.126][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[2024-06-26 21:05:01.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.252][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-26 21:05:01.253][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-26 21:05:01.255][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-26 21:05:01.256][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-26 21:05:01.257][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 21:05:01.258][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-26 21:05:01.260][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-26 21:05:01.261][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-26 21:05:01.262][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-26 21:05:01.264][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-26 21:05:01.265][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 21:05:01.266][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-26 21:05:01.267][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-26 21:05:01.269][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-26 21:05:01.270][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-26 21:05:01.271][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 21:05:01.272][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-26 21:05:01.274][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-26 21:05:01.275][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 21:05:01.276][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-26 21:05:01.278][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-26 21:05:01.279][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-26 21:05:01.280][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-26 21:05:01.282][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-26 21:05:01.283][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-26 21:05:01.284][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-26 21:05:01.285][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-26 21:05:01.287][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-26 21:05:01.288][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-26 21:05:01.289][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-26 21:05:01.291][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-26 21:05:01.292][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-26 21:05:01.293][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-26 21:05:01.295][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-26 21:05:01.296][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-26 21:05:01.297][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-26 21:05:01.298][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-26 21:05:01.300][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-26 21:05:01.301][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-26 21:05:01.302][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-26 21:05:01.303][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-26 21:05:01.305][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-26 21:05:01.306][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-26 21:05:01.307][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-26 21:05:01.309][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-26 21:05:01.310][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-26 21:05:01.311][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-26 21:05:01.312][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-26 21:05:01.314][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-26 21:05:01.315][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-26 21:05:01.316][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-26 21:05:01.318][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-26 21:05:01.319][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-26 21:05:01.320][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-26 21:05:01.321][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-26 21:05:01.323][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-26 21:05:01.324][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-26 21:05:01.326][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-26 21:05:01.327][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-26 21:05:01.328][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-26 21:05:01.329][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-26 21:05:01.331][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-26 21:05:01.332][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-26 21:05:01.333][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-26 21:05:01.335][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-26 21:05:01.336][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-26 21:05:01.337][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 21:05:01.339][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 21:05:01.340][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-26 21:05:01.341][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-26 21:05:01.343][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-26 21:05:01.344][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-26 21:05:01.345][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-26 21:05:01.347][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-26 21:05:01.348][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-26 21:05:01.349][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-26 21:05:01.351][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-26 21:05:01.352][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-26 21:05:01.353][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-26 21:05:01.355][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-26 21:05:01.356][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-26 21:05:01.357][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-26 21:05:01.359][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-26 21:05:01.360][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-26 21:05:01.362][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:05:01.363][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:05:01.363][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.365][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:01.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:01.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:01.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:01.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:01.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:01.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:01.467][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[2024-06-26 21:05:01.468][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-26 21:05:01.470][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 21:05:01.471][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.472][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.473][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.474][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:05:01.475][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.476][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.477][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.478][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.479][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:05:01.480][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:05:01.482][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.483][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-26 21:05:01.484][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:05:01.485][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-26 21:05:01.485][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-26 21:05:01.485][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-26 21:05:01.485][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-26 21:05:01.485][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-26 21:05:01.485][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-26 21:05:01.485][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-26 21:05:01.485][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-26 21:05:01.485][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-26 21:05:01.486][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:01.487][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:05:01.487][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:05:01.488][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:05:01.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:01.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:01.502][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:05:01.503][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:01.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:01.504][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:05:01.505][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 21:05:01.505][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-26 21:05:01.506][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:05:01.507][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:05:01.508][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:01.509][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:01.510][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-26 21:05:01.511][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 21:05:01.514][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 21:05:01.515][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-26 21:05:01.516][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 21:05:01.518][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-26 21:05:01.519][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-26 21:05:01.520][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-26 21:05:01.521][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-26 21:05:01.522][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-26 21:05:01.524][biodb::testThat]
biodb.INFO [2024-06-26 21:05:01.524][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-06-26 21:05:01.525][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:05:01.526][biodb::testThat]
biodb.DEBUG[2024-06-26 21:05:01.530][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-06-26 21:05:01.534][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:05:01.535][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:05:01.536][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-06-26 21:05:02.167][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[2024-06-26 21:05:03.047][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:05:03.049][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-06-26 21:05:03.053][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-06-26 21:05:03.099][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[2024-06-26 21:05:03.102][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:05:03.103][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:05:03.105][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-06-26 21:05:03.733][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-06-26 21:05:04.749][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:05:04.751][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-06-26 21:05:04.755][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-06-26 21:05:04.766][biodb::testThat]
biodb.INFO [2024-06-26 21:05:04.767][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-06-26 21:05:04.768][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:05:04.769][biodb::testThat]
biodb.INFO [2024-06-26 21:05:04.798][biodb::testThat]
biodb.INFO [2024-06-26 21:05:04.799][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-06-26 21:05:04.800][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:05:04.801][biodb::testThat]
biodb.DEBUG[2024-06-26 21:05:04.805][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-06-26 21:05:04.808][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:05:04.809][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:05:04.811][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-06-26 21:05:05.279][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-06-26 21:05:05.777][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:05:05.781][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-06-26 21:05:05.788][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-06-26 21:05:05.798][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[2024-06-26 21:05:05.803][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:05:05.806][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-06-26 21:05:05.808][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:05:05.811][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-06-26 21:05:05.821][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[2024-06-26 21:05:05.827][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:05:05.828][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:05:05.831][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-06-26 21:05:06.331][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-06-26 21:05:06.807][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:05:06.811][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-06-26 21:05:06.817][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-06-26 21:05:06.830][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-06-26 21:05:06.834][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:05:06.836][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:05:06.838][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-06-26 21:05:08.086][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-06-26 21:05:10.865][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:05:10.868][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-06-26 21:05:10.874][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-06-26 21:05:11.021][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[2024-06-26 21:05:11.025][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-26 21:05:11.026][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-26 21:05:11.029][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-06-26 21:05:12.257][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-06-26 21:05:15.192][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-26 21:05:15.195][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-06-26 21:05:15.201][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-06-26 21:05:15.332][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-26 21:05:15.334][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-26 21:05:15.336][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-26 21:05:15.337][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-26 21:05:15.338][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.340][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.342][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-26 21:05:15.348][biodb::testContext]
biodb.INFO [2024-06-26 21:05:15.349][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:05:15.350][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-06-26 21:05:15.351][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-26 21:05:15.352][biodb::testContext]
biodb.INFO [2024-06-26 21:05:15.354][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:05:15.356][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-26 21:05:15.361][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:05:15.362][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-26 21:05:15.363][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-26 21:05:15.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.367][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-26 21:05:15.368][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-26 21:05:15.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.373][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-26 21:05:15.374][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-26 21:05:15.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.378][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-26 21:05:15.379][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-26 21:05:15.380][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-26 21:05:15.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.384][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-26 21:05:15.385][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-26 21:05:15.386][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-26 21:05:15.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.390][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-26 21:05:15.391][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-26 21:05:15.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.395][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-26 21:05:15.396][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-26 21:05:15.397][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-26 21:05:15.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.449][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-26 21:05:15.450][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-26 21:05:15.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.454][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-26 21:05:15.456][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-26 21:05:15.457][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-26 21:05:15.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.460][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[2024-06-26 21:05:15.461][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:05:15.462][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-26 21:05:15.463][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-26 21:05:15.465][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-26 21:05:15.466][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-26 21:05:15.467][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-26 21:05:15.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.471][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-26 21:05:15.472][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-26 21:05:15.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.475][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[2024-06-26 21:05:15.477][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-26 21:05:15.478][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-26 21:05:15.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.482][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-26 21:05:15.483][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-26 21:05:15.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.486][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[2024-06-26 21:05:15.487][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-26 21:05:15.488][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-26 21:05:15.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.492][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-26 21:05:15.494][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-26 21:05:15.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.497][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[2024-06-26 21:05:15.498][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-26 21:05:15.499][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-26 21:05:15.503][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-26 21:05:15.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.507][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-26 21:05:15.509][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-26 21:05:15.510][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-26 21:05:15.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.514][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-26 21:05:15.516][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.517][self$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[2024-06-26 21:05:15.518][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.519][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:05:15.520][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.521][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.523][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.524][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.525][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:05:15.526][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:05:15.527][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.528][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-26 21:05:15.529][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:05:15.530][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.531][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.532][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:05:15.532][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:05:15.532][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:05:15.532][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:05:15.532][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:05:15.533][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:05:15.534][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:15.535][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:15.536][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:05:15.537][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:15.538][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:15.539][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.540][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.541][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:05:15.542][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:05:15.543][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.544][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.545][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-26 21:05:15.547][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.549][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:05:15.550][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.551][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:05:15.552][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.553][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.555][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.556][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.558][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:05:15.559][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:05:15.560][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.561][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-26 21:05:15.562][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:05:15.564][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.565][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.566][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:05:15.566][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:05:15.566][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-26 21:05:15.566][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-26 21:05:15.566][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-26 21:05:15.567][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:05:15.569][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:15.570][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:15.571][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:05:15.572][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:15.573][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:15.574][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.575][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.577][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:05:15.578][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:05:15.579][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.580][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.582][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-26 21:05:15.584][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.585][self$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[2024-06-26 21:05:15.587][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.588][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:05:15.589][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.590][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.591][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.593][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.594][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:05:15.595][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:05:15.596][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.597][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-26 21:05:15.599][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:05:15.600][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.601][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.602][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.603][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:05:15.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:15.605][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:15.606][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:05:15.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:15.609][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:15.610][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.611][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.612][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:05:15.613][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:05:15.614][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.616][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.617][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-26 21:05:15.620][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.621][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-26 21:05:15.622][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.623][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:05:15.624][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.625][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.627][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.628][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.629][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-26 21:05:15.630][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:05:15.631][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.632][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-26 21:05:15.633][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:05:15.634][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.635][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.636][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.637][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:05:15.638][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:15.639][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:15.640][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:05:15.642][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:15.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:15.644][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.645][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.646][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:05:15.647][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:05:15.648][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.649][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:15.651][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:05:15.652][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.668][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[2024-06-26 21:05:15.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.702][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[2024-06-26 21:05:15.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.706][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[2024-06-26 21:05:15.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.711][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[2024-06-26 21:05:15.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.734][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-26 21:05:15.735][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-26 21:05:15.736][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-26 21:05:15.738][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-26 21:05:15.739][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-26 21:05:15.741][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-26 21:05:15.742][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-26 21:05:15.744][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-26 21:05:15.745][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-26 21:05:15.746][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-26 21:05:15.748][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-26 21:05:15.749][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-26 21:05:15.750][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-26 21:05:15.752][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-26 21:05:15.753][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-26 21:05:15.755][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 21:05:15.756][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-26 21:05:15.757][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-26 21:05:15.759][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-26 21:05:15.760][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-26 21:05:15.761][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-26 21:05:15.763][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-26 21:05:15.764][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-26 21:05:15.766][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-26 21:05:15.767][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-26 21:05:15.769][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-26 21:05:15.770][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-26 21:05:15.771][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-26 21:05:15.773][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-26 21:05:15.774][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-26 21:05:15.776][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-26 21:05:15.777][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-26 21:05:15.778][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-26 21:05:15.780][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-26 21:05:15.781][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-26 21:05:15.783][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-26 21:05:15.784][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-26 21:05:15.786][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-26 21:05:15.787][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-26 21:05:15.789][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-26 21:05:15.790][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-26 21:05:15.792][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-26 21:05:15.805][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-26 21:05:15.807][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-26 21:05:15.808][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-26 21:05:15.810][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-26 21:05:15.811][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-26 21:05:15.813][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-26 21:05:15.814][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-26 21:05:15.815][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-26 21:05:15.817][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-26 21:05:15.818][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-26 21:05:15.820][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-26 21:05:15.821][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-26 21:05:15.822][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-26 21:05:15.824][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-26 21:05:15.825][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-26 21:05:15.827][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-26 21:05:15.828][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-26 21:05:15.829][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-26 21:05:15.831][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-26 21:05:15.832][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-26 21:05:15.833][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-26 21:05:15.835][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-26 21:05:15.836][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-26 21:05:15.837][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-26 21:05:15.839][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-26 21:05:15.840][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-26 21:05:15.841][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-26 21:05:15.843][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-26 21:05:15.844][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-26 21:05:15.845][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-26 21:05:15.846][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-26 21:05:15.848][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-26 21:05:15.849][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-26 21:05:15.850][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-26 21:05:15.852][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-26 21:05:15.853][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-26 21:05:15.854][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-26 21:05:15.856][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-26 21:05:15.857][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-26 21:05:15.858][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-26 21:05:15.860][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-26 21:05:15.861][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-26 21:05:15.863][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-26 21:05:15.864][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-26 21:05:15.865][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.866][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.897][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[2024-06-26 21:05:15.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.950][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[2024-06-26 21:05:15.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.957][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[2024-06-26 21:05:15.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-26 21:05:15.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-26 21:05:15.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:15.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:15.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:15.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:15.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:15.969][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[2024-06-26 21:05:15.970][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-06-26 21:05:15.972][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 21:05:15.974][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.975][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.976][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.977][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-26 21:05:15.978][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.979][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.980][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.981][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.982][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-26 21:05:15.983][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-26 21:05:15.984][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:15.985][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-06-26 21:05:15.986][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-26 21:05:15.987][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-06-26 21:05:15.987][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-06-26 21:05:15.987][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-06-26 21:05:15.987][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-06-26 21:05:15.987][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-06-26 21:05:15.987][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-06-26 21:05:15.987][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-06-26 21:05:15.987][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-06-26 21:05:15.987][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-06-26 21:05:15.988][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-26 21:05:15.989][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-26 21:05:15.989][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-26 21:05:15.990][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-26 21:05:15.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:15.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:15.992][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-26 21:05:15.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-26 21:05:15.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-26 21:05:15.995][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-26 21:05:15.996][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-06-26 21:05:15.996][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-06-26 21:05:15.997][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-26 21:05:15.998][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-26 21:05:15.999][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-26 21:05:16.000][self$setPropertyValue]
biodb.DEBUG[2024-06-26 21:05:16.001][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-06-26 21:05:16.003][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-26 21:05:16.006][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 21:05:16.007][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-06-26 21:05:16.008][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-06-26 21:05:16.010][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-06-26 21:05:16.011][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-26 21:05:16.012][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-06-26 21:05:16.013][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-06-26 21:05:16.014][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-06-26 21:05:16.016][biodb::testThat]
biodb.INFO [2024-06-26 21:05:16.017][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2024-06-26 21:05:16.017][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-26 21:05:16.018][biodb::testThat]
biodb.DEBUG[2024-06-26 21:05:16.022][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-06-26 21:05:16.026][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-26 21:05:16.036][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-06-26 21:05:16.038][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-26 21:05:16.087][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-06-26 21:05:17.005][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-06-26 21:05:17.007][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-26 21:05:17.009][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-06-26 21:05:17.010][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-06-26 21:05:17.012][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-06-26 21:05:17.014][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-06-26 21:05:17.015][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-06-26 21:05:17.016][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-06-26 21:05:17.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:05:17.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:17.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:17.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:17.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:17.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:17.029][FUN] Functions in observer BiodbConfig: [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[2024-06-26 21:05:17.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.059][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 21:05:17.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 21:05:17.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.063][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:05:17.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:05:17.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.068][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.073][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.078][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.088][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 21:05:17.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.093][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 21:05:17.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.098][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.103][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.118][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 21:05:17.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.122][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-26 21:05:17.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.131][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.135][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 21:05:17.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.156][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.161][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.165][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.175][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:05:17.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:05:17.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:17.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:17.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:17.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:17.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:17.204][FUN] Functions in observer BiodbConfig: [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[2024-06-26 21:05:17.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.229][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 21:05:17.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-26 21:05:17.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.233][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:05:17.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-26 21:05:17.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.238][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.243][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.248][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.252][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.257][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 21:05:17.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.261][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-06-26 21:05:17.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.266][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.271][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.280][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.284][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 21:05:17.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.289][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-06-26 21:05:17.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.293][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.298][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.303][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-06-26 21:05:17.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.308][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.312][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.322][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-26 21:05:17.388][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-06-26 21:05:17.391][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-26 21:05:17.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:05:17.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:17.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:17.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:17.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:17.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:17.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-26 21:05:17.406][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:05:17.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:05:17.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.411][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:05:17.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:05:17.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.415][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-26 21:05:17.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-26 21:05:17.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.419][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-26 21:05:17.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-26 21:05:17.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.422][private$selectFields] Fields none
biodb.TRACE[2024-06-26 21:05:17.423][private$selectFields]
biodb.TRACE[2024-06-26 21:05:17.424][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-06-26 21:05:17.425][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:05:17.426][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:05:17.427][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.428][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.430][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.430][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.431][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.433][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.434][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.435][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.437][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.438][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.439][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.440][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.441][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.442][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.444][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.445][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.446][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.448][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.449][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.450][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.451][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.452][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.453][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.455][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.456][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.457][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.459][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.460][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.461][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.462][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.463][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.464][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.466][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.467][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.468][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.470][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.471][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.471][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.473][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.474][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.475][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.477][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.478][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.479][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.481][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.481][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.482][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.484][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.485][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:05:17.486][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:05:17.487][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.488][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.490][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.491][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.491][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.493][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.494][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.495][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.497][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.498][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.499][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.500][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.501][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.502][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.504][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.505][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.506][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.508][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.508][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.509][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.511][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.512][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.513][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.515][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.516][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-06-26 21:05:17.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.540][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.544][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.547][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.551][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.555][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.574][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.578][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.582][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.597][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.601][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.605][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.614][private$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[2024-06-26 21:05:17.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-26 21:05:17.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:17.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:17.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:17.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:17.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:17.663][FUN] Functions in observer BiodbConfig: [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[2024-06-26 21:05:17.665][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:05:17.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:05:17.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.669][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-26 21:05:17.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-26 21:05:17.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.673][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-26 21:05:17.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-26 21:05:17.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.676][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-26 21:05:17.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-26 21:05:17.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.680][private$selectFields] Fields none
biodb.TRACE[2024-06-26 21:05:17.681][private$selectFields]
biodb.TRACE[2024-06-26 21:05:17.682][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-06-26 21:05:17.683][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-26 21:05:17.684][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:05:17.685][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.686][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.687][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.688][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.689][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.691][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.692][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.693][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.695][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.696][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.697][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.698][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.699][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.700][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.702][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.703][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.704][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.706][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.707][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.708][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.710][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.711][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.712][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.712][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.713][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.714][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.715][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.717][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.718][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.719][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.721][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.722][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.736][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.738][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.739][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.740][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.742][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.743][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.744][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.746][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.747][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.748][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.750][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.751][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.752][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.753][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.754][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.755][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.757][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.758][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:05:17.759][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-06-26 21:05:17.760][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.761][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.763][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.763][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.764][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.766][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.767][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.768][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.770][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.771][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.772][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.774][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.774][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.775][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.777][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.778][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.779][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.781][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.782][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.783][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.785][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.786][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.787][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.788][ef$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.789][private$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[2024-06-26 21:05:17.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-26 21:05:17.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-26 21:05:17.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-26 21:05:17.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.813][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.816][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.820][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-26 21:05:17.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.824][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.828][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.831][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-26 21:05:17.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-26 21:05:17.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.846][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.854][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-26 21:05:17.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-26 21:05:17.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-26 21:05:17.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-26 21:05:17.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.869][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.872][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.876][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-06-26 21:05:17.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-26 21:05:17.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-26 21:05:17.883][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-06-26 21:05:17.884][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-06-26 21:05:17.885][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-06-26 21:05:17.891][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-26 21:05:17.892][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-06-26 21:05:17.893][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-06-26 21:05:17.894][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-26 21:05:17.894][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-26 21:05:17.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-26 21:05:17.896][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-26 21:05:17.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-26 21:05:17.898][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-26 21:05:17.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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
LipidmapsStructureConn0.9980.0643.314
LipidmapsStructureEntry0.1270.0000.128