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This page was generated on 2023-11-02 11:40:27 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 200/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbLipidmaps 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/biodbLipidmaps
git_branch: RELEASE_3_18
git_last_commit: f02eedd
git_last_commit_date: 2023-10-24 11:38:15 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for biodbLipidmaps on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: biodbLipidmaps
Version: 1.8.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings biodbLipidmaps_1.8.0.tar.gz
StartedAt: 2023-11-02 08:45:29 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 08:50:48 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 319.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbLipidmaps.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings biodbLipidmaps_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbLipidmaps’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
LipidmapsStructureConn 1.025  0.083   5.146
* 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:
          name = request.key, ext = "request")
  }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(db = `<LpdmpsSC>`, opt = `<named list>`)
   3.   └─db$searchCompound(...)
   4.     └─self$searchForEntries(fields, max.results = max.results)
   5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
   6.         └─self$wsLmsdSearch(...)
   7.           └─self$getBiodb()$getRequestScheduler()$sendRequest(request)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 155 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

Installation output

biodbLipidmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL biodbLipidmaps
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbLipidmaps)

Tests output

biodbLipidmaps.Rcheck/tests/testthat.Rout.fail


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2023-11-02 08:46:34.376][biodb::testContext]
biodb.INFO [2023-11-02 08:46:34.379][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:46:34.381][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-11-02 08:46:34.382][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:46:34.383][biodb::testContext]
biodb.INFO [2023-11-02 08:46:34.392][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:46:34.395][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-11-02 08:46:34.404][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:46:34.406][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-11-02 08:46:34.407][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-11-02 08:46:34.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.413][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-11-02 08:46:34.441][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-11-02 08:46:34.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.446][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-11-02 08:46:34.448][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-11-02 08:46:34.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.453][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-11-02 08:46:34.455][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-11-02 08:46:34.456][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-11-02 08:46:34.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.460][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[2023-11-02 08:46:34.462][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-11-02 08:46:34.463][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-11-02 08:46:34.465][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-11-02 08:46:34.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.470][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-11-02 08:46:34.471][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-11-02 08:46:34.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.475][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[2023-11-02 08:46:34.477][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-11-02 08:46:34.478][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-11-02 08:46:34.480][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-11-02 08:46:34.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.485][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-11-02 08:46:34.487][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-11-02 08:46:34.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.492][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-11-02 08:46:34.493][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-11-02 08:46:34.495][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-11-02 08:46:34.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.500][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:46:34.502][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-11-02 08:46:34.503][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-11-02 08:46:34.505][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-11-02 08:46:34.506][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-11-02 08:46:34.508][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-11-02 08:46:34.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.513][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-11-02 08:46:34.515][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-11-02 08:46:34.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.520][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-11-02 08:46:34.521][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-11-02 08:46:34.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.527][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-11-02 08:46:34.528][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-11-02 08:46:34.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.534][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-11-02 08:46:34.535][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-11-02 08:46:34.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.540][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-11-02 08:46:34.542][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-11-02 08:46:34.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.547][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:46:34.549][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-11-02 08:46:34.554][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-11-02 08:46:34.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.558][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[2023-11-02 08:46:34.560][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-11-02 08:46:34.561][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-11-02 08:46:34.563][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-11-02 08:46:34.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.572][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-11-02 08:46:34.621][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:34.645][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-11-02 08:46:34.647][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.649][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:46:34.650][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.652][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:46:34.653][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:34.655][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:46:34.656][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:46:34.657][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:46:34.659][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.671][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-11-02 08:46:34.672][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:46:34.674][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.675][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.677][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:46:34.677][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:46:34.677][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:46:34.677][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:46:34.677][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:46:34.678][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:46:34.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:46:34.681][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:46:34.682][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:46:34.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:46:34.685][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:46:34.686][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:46:34.687][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.689][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:46:34.690][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:46:34.691][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:34.693][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.694][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-11-02 08:46:34.697][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:34.698][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:46:34.700][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.701][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:46:34.703][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.704][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:46:34.705][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:34.707][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:46:34.708][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:46:34.710][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:46:34.711][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.712][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-11-02 08:46:34.714][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:46:34.715][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.717][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.718][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:46:34.718][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:46:34.718][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:46:34.718][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:46:34.718][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:46:34.719][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:46:34.721][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:46:34.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:46:34.723][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:46:34.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:46:34.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:46:34.727][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:46:34.729][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.730][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:46:34.731][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:46:34.733][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:34.734][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.736][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-11-02 08:46:34.738][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.739][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-11-02 08:46:34.741][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.742][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:46:34.744][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.745][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:46:34.746][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:34.748][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:46:34.749][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:46:34.751][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:46:34.752][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:34.753][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-11-02 08:46:34.755][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:46:34.756][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.758][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.759][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.761][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:46:34.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:46:34.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:46:34.765][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:46:34.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:46:34.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:46:34.769][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:46:34.771][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.772][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:46:34.774][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:46:34.775][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:34.777][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.778][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-11-02 08:46:34.781][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.783][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:46:34.784][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.786][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:46:34.787][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.789][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:46:34.790][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:34.792][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:46:34.793][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:46:34.794][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:46:34.796][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:34.797][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-11-02 08:46:34.799][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:46:34.800][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.802][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:34.803][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.804][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:46:34.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:46:34.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:46:34.808][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:46:34.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:46:34.811][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:46:34.813][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:46:34.814][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.815][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:46:34.817][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:46:34.818][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:34.819][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:34.825][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:46:34.826][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.866][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[2023-11-02 08:46:34.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.929][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[2023-11-02 08:46:34.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:34.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:34.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:34.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:34.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:34.937][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-11-02 08:46:34.943][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-11-02 08:46:34.945][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-11-02 08:46:34.947][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-11-02 08:46:34.949][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-11-02 08:46:34.951][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-11-02 08:46:34.953][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-11-02 08:46:34.955][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-11-02 08:46:34.957][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-11-02 08:46:34.959][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-11-02 08:46:34.961][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-11-02 08:46:34.964][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-11-02 08:46:34.966][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-11-02 08:46:34.968][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-11-02 08:46:34.970][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-11-02 08:46:34.972][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-11-02 08:46:34.974][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-11-02 08:46:34.976][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-11-02 08:46:34.978][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-11-02 08:46:34.980][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-11-02 08:46:34.982][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-11-02 08:46:34.984][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-11-02 08:46:34.986][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-11-02 08:46:34.988][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-11-02 08:46:34.990][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-11-02 08:46:34.992][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-11-02 08:46:34.994][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-11-02 08:46:34.996][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-11-02 08:46:34.998][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-11-02 08:46:35.000][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-11-02 08:46:35.002][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-11-02 08:46:35.004][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-11-02 08:46:35.006][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-11-02 08:46:35.008][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-11-02 08:46:35.010][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-11-02 08:46:35.012][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-11-02 08:46:35.014][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-11-02 08:46:35.016][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-11-02 08:46:35.018][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-11-02 08:46:35.020][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-11-02 08:46:35.022][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-11-02 08:46:35.024][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-11-02 08:46:35.026][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-11-02 08:46:35.029][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-11-02 08:46:35.031][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-11-02 08:46:35.033][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-11-02 08:46:35.035][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-11-02 08:46:35.037][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-11-02 08:46:35.039][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-11-02 08:46:35.041][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-11-02 08:46:35.043][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-11-02 08:46:35.045][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-11-02 08:46:35.055][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-11-02 08:46:35.057][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-11-02 08:46:35.059][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-11-02 08:46:35.062][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-11-02 08:46:35.064][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-11-02 08:46:35.066][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-11-02 08:46:35.068][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-11-02 08:46:35.070][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-11-02 08:46:35.072][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-11-02 08:46:35.074][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-11-02 08:46:35.076][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-11-02 08:46:35.078][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-11-02 08:46:35.080][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-11-02 08:46:35.082][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-11-02 08:46:35.084][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-11-02 08:46:35.086][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-11-02 08:46:35.088][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-11-02 08:46:35.090][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-11-02 08:46:35.092][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-11-02 08:46:35.094][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-11-02 08:46:35.096][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-11-02 08:46:35.098][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-11-02 08:46:35.100][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-11-02 08:46:35.102][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-11-02 08:46:35.104][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-11-02 08:46:35.106][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-11-02 08:46:35.108][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-11-02 08:46:35.110][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-11-02 08:46:35.112][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-11-02 08:46:35.114][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-11-02 08:46:35.116][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-11-02 08:46:35.124][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-11-02 08:46:35.126][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:46:35.131][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:46:35.132][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.135][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.204][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.DEBUG[2023-11-02 08:46:35.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.222][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[2023-11-02 08:46:35.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.276][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[2023-11-02 08:46:35.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:46:35.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:46:35.298][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-11-02 08:46:35.311][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-11-02 08:46:35.314][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:35.315][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-11-02 08:46:35.317][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:35.318][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:46:35.319][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:35.321][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:46:35.322][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:35.324][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:46:35.325][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:46:35.326][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:46:35.328][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:35.329][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-11-02 08:46:35.331][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:46:35.332][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-11-02 08:46:35.332][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-11-02 08:46:35.332][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-11-02 08:46:35.332][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-11-02 08:46:35.332][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-11-02 08:46:35.332][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-11-02 08:46:35.332][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-11-02 08:46:35.332][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-11-02 08:46:35.332][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-11-02 08:46:35.334][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-11-02 08:46:35.335][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:46:35.335][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:46:35.336][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:46:35.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:46:35.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:46:35.340][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:46:35.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:46:35.343][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:46:35.344][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:46:35.346][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-11-02 08:46:35.346][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-11-02 08:46:35.347][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:46:35.349][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:46:35.350][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-11-02 08:46:35.351][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:46:35.360][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-11-02 08:46:35.362][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-11-02 08:46:35.393][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-11-02 08:46:35.395][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-11-02 08:46:35.400][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-11-02 08:46:35.406][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-11-02 08:46:35.412][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-11-02 08:46:35.413][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-11-02 08:46:35.415][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-11-02 08:46:35.416][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-11-02 08:46:35.428][biodb::testThat]
biodb.INFO [2023-11-02 08:46:35.430][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-11-02 08:46:35.431][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:46:35.433][biodb::testThat]
biodb.TRACE[2023-11-02 08:46:35.439][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-4.3.1/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-11-02 08:46:35.453][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:35.458][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-11-02 08:46:35.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:35.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:35.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:35.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:35.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:35.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:35.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:35.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:35.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:35.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.547][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:46:35.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:46:35.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.553][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:35.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:35.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.558][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:35.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:35.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.601][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:35.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:35.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.608][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:35.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:35.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.613][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:35.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:35.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.619][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:46:35.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:35.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.625][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:46:35.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:35.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.631][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:35.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:35.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.637][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:35.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:35.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:35.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:35.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:35.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:35.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.655][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:46:35.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:35.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.660][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-11-02 08:46:35.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:35.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.666][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:35.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:35.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:35.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:35.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.678][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:46:35.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:35.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:35.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:35.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:35.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:35.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:35.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:35.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:35.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:35.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:35.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:35.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.795][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.801][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.812][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:35.853][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-11-02 08:46:35.856][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:46:35.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:46:35.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.862][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:46:35.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:46:35.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.868][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-11-02 08:46:35.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-11-02 08:46:35.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.873][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-11-02 08:46:35.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-11-02 08:46:35.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.923][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:35.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:35.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.974][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.980][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:35.985][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:35.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:35.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.021][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.022][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.024][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.025][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.057][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.062][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.064][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.065][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.067][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.087][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.092][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.098][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.104][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.105][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.106][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.108][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.109][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.136][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:36.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:36.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.142][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:36.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:36.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.148][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:36.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:36.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.153][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:36.154][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:36.156][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.157][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.158][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:36.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:36.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.194][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.196][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.197][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.198][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.218][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.224][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.229][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.235][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.236][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.238][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.239][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.240][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.259][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.261][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.262][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.263][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.272][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.274][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.275][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.276][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.285][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:36.287][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:36.288][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.289][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.298][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.299][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.301][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.302][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.311][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.312][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.314][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.315][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.324][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.325][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.327][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.328][ef$get] fields variable is a list.
biodb.INFO [2023-11-02 08:46:36.343][biodb::testThat]
biodb.INFO [2023-11-02 08:46:36.344][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-11-02 08:46:36.345][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:46:36.347][biodb::testThat]
biodb.DEBUG[2023-11-02 08:46:36.367][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-11-02 08:46:36.376][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:46:36.381][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-11-02 08:46:36.383][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:46:36.385][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-11-02 08:46:36.387][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:46:36.420][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:46:36.421][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-11-02 08:46:36.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:46:36.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:46:36.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:46:36.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:46:36.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:46:36.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:46:36.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:46:36.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:36.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:36.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:46:36.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:46:36.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.503][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:46:36.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:46:36.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.509][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:36.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:46:36.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.515][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.521][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:46:36.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.526][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.532][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:46:36.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.538][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:46:36.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.543][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:46:36.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:36.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.549][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:36.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:36.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.555][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:46:36.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:46:36.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.560][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.566][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.572][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:46:36.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.578][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-11-02 08:46:36.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.594][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:46:36.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.600][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.622][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.628][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:36.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:36.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.633][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:36.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:36.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.647][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:36.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:46:36.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:46:36.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:46:36.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:36.686][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-11-02 08:46:36.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-11-02 08:46:36.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-11-02 08:46:36.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-11-02 08:46:36.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-11-02 08:46:36.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-11-02 08:46:36.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-11-02 08:46:36.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-11-02 08:46:36.717][biodb::testThat]
biodb.INFO [2023-11-02 08:46:36.718][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-11-02 08:46:36.720][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:46:36.721][biodb::testThat]
biodb.TRACE[2023-11-02 08:46:36.725][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.727][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.728][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.729][ef$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:36.731][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-11-02 08:46:36.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:36.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:36.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:36.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:36.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:36.802][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-11-02 08:46:36.809][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[2023-11-02 08:46:36.840][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:36.842][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:36.844][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-11-02 08:46:38.266][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-11-02 08:46:39.521][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:46:39.524][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-11-02 08:46:39.547][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-11-02 08:46:39.550][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-11-02 08:46:39.575][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:39.577][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:39.579][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.580][ef$get] fields variable is a list.
biodb.INFO [2023-11-02 08:46:39.588][biodb::testThat]
biodb.INFO [2023-11-02 08:46:39.590][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-11-02 08:46:39.591][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:46:39.593][biodb::testThat]
biodb.TRACE[2023-11-02 08:46:39.656][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:39.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:39.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.663][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:39.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:39.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:39.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:39.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:39.842][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-11-02 08:46:39.847][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:46:39.872][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-11-02 08:46:39.874][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:46:39.876][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-11-02 08:46:39.917][biodb::testThat]
biodb.INFO [2023-11-02 08:46:39.919][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-11-02 08:46:39.921][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:46:39.922][biodb::testThat]
biodb.TRACE[2023-11-02 08:46:39.955][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:46:39.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:46:39.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.961][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:46:39.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:46:39.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.966][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-11-02 08:46:39.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-11-02 08:46:39.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:39.972][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-11-02 08:46:39.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-11-02 08:46:39.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:39.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:40.039][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:46:40.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:46:40.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:40.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:40.045][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:46:40.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:46:40.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:40.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:40.050][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-11-02 08:46:40.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-11-02 08:46:40.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:40.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:40.056][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-11-02 08:46:40.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-11-02 08:46:40.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:40.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-11-02 08:46:40.072][biodb::testThat]
biodb.INFO [2023-11-02 08:46:40.073][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-11-02 08:46:40.075][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:46:40.076][biodb::testThat]
biodb.INFO [2023-11-02 08:46:40.090][biodb::testThat]
biodb.INFO [2023-11-02 08:46:40.091][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-11-02 08:46:40.092][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:46:40.094][biodb::testThat]
biodb.INFO [2023-11-02 08:46:40.107][biodb::testThat]
biodb.INFO [2023-11-02 08:46:40.108][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-11-02 08:46:40.109][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:46:40.111][biodb::testThat]
biodb.DEBUG[2023-11-02 08:46:40.117][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-11-02 08:46:45.196][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-11-02 08:46:46.240][biodb::testThat]
biodb.INFO [2023-11-02 08:46:46.241][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-11-02 08:46:46.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:46:46.244][biodb::testThat]
biodb.TRACE[2023-11-02 08:46:46.268][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:46.270][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:46.271][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:46.273][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:46.274][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:46.276][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:46.277][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:46.278][ef$get] fields variable is a list.
biodb.INFO [2023-11-02 08:46:46.281][biodb::testThat]
biodb.INFO [2023-11-02 08:46:46.282][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-11-02 08:46:46.284][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:46:46.285][biodb::testThat]
biodb.TRACE[2023-11-02 08:46:46.305][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:46.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:46.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:46.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:46.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:46.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:46.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:46.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:46.316][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:46:46.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:46:46.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:46.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:46.440][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-11-02 08:46:46.451][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:46:46.453][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-11-02 08:46:46.455][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:46:46.457][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-11-02 08:46:46.658][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-11-02 08:46:46.667][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:46:46.669][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-11-02 08:46:46.672][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:46:46.674][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-11-02 08:46:46.706][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-11-02 08:46:46.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-11-02 08:46:46.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:46.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:46.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:46.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:46:46.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:46.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:46.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:46.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:46.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:46.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:46.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:46.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:46.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:46.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:46.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:46.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:46.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:46.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:46.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:46.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:46.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:46.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:46:46.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:46.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:46:46.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:46:46.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:46:46.793][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-11-02 08:46:46.826][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:46:46.828][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:46:46.861][private$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[2023-11-02 08:46:51.899][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.INFO [2023-11-02 08:47:52.632][biodb::testThat]
biodb.INFO [2023-11-02 08:47:52.634][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-11-02 08:47:52.636][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:47:52.637][biodb::testThat]
biodb.TRACE[2023-11-02 08:47:52.643][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-11-02 08:47:52.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-11-02 08:47:52.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:52.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:52.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:52.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:47:52.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:52.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:52.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:52.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:52.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:52.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:52.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:52.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:52.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:52.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:52.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:52.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:52.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:52.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:47:52.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:52.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:47:52.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:47:52.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:47:52.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:47:52.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:47:52.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:47:52.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:47:52.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:47:52.715][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:47:52.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:47:52.721][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[2023-11-02 08:47:52.727][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:47:52.729][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:47:52.731][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2023-11-02 08:47:57.474][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2023-11-02 08:48:32.332][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:48:32.335][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-11-02 08:48:32.368][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-11-02 08:48:33.633][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-11-02 08:48:33.711][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-11-02 08:48:33.713][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-11-02 08:48:33.715][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-11-02 08:48:33.717][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:48:33.718][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:48:33.720][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-11-02 08:48:33.721][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:48:33.723][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:48:33.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:33.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:33.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:33.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:33.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:33.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:33.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:33.765][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-11-02 08:48:33.769][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:48:33.771][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:48:33.773][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-11-02 08:48:35.014][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-11-02 08:48:36.206][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:48:36.209][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-11-02 08:48:36.214][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-11-02 08:48:36.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:36.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:36.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:36.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:36.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:36.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:36.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:48:36.235][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-11-02 08:48:36.239][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:48:36.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:48:36.243][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-11-02 08:48:37.462][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-11-02 08:48:38.674][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:48:38.677][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-11-02 08:48:38.681][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-11-02 08:48:38.685][private$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[2023-11-02 08:48:38.687][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:48:38.689][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-11-02 08:48:38.691][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-11-02 08:48:38.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:38.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:38.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:38.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:38.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:38.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:38.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:48:38.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:38.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:38.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:38.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:38.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:38.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:38.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:38.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:38.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.766][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:48:38.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:48:38.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.772][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:38.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:38.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.777][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:48:38.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:48:38.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.783][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:48:38.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:48:38.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.788][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:48:38.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:48:38.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.794][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:48:38.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:48:38.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.799][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:48:38.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:38.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.805][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:48:38.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:38.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.810][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:48:38.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:48:38.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.816][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:48:38.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:48:38.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:38.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:38.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.827][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:38.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:38.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.832][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:48:38.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:38.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.838][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-11-02 08:48:38.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:38.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.843][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:38.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:38.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:38.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:38.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.854][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:48:38.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:38.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.859][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:38.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:38.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.865][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:38.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:38.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:38.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:38.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.875][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:38.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:38.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:38.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:38.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:38.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:38.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:38.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:38.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:48:38.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:38.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:38.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:38.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:38.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:38.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:38.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:48:38.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:38.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:38.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:38.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:38.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:48:38.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:48:38.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.937][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:48:38.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:48:38.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.961][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:38.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:48:38.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.966][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:48:38.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:48:38.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.971][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:48:38.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:48:38.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.977][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:48:38.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:48:38.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.982][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:48:38.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:48:38.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.988][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:48:38.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:38.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.993][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:48:38.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:38.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:38.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:38.998][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:48:39.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:48:39.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.004][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:48:39.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:48:39.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:39.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:39.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:39.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:39.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.020][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:48:39.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:39.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.025][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-11-02 08:48:39.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:39.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:39.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:39.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:48:39.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:39.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.041][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:48:39.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:48:39.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.046][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.052][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:39.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:39.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.062][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:39.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:39.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:39.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:39.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:39.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:39.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:39.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:39.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:39.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:39.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:39.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:39.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:39.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:39.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:39.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:39.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:48:39.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:48:39.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:48:39.115][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-11-02 08:48:39.130][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-11-02 08:48:39.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:39.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:39.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:39.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:39.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:39.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:39.147][FUN] Functions in observer BiodbConfig: [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[2023-11-02 08:48:39.148][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.154][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.176][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:48:39.178][private$selectFields]
biodb.TRACE[2023-11-02 08:48:39.179][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:48:39.180][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:48:39.181][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:48:39.183][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.184][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.185][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.187][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.188][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.189][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.191][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.192][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.193][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:48:39.194][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:48:39.196][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.197][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.199][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.200][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.201][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-11-02 08:48:39.202][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.208][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.213][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.230][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-11-02 08:48:39.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:39.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:39.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:39.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:39.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:39.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:39.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:48:39.248][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.253][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.258][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:48:39.260][private$selectFields]
biodb.TRACE[2023-11-02 08:48:39.261][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:48:39.262][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:48:39.263][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:48:39.265][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.266][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.267][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.268][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.270][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.271][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.272][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.274][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.275][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:48:39.276][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:48:39.277][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.279][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.280][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.281][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.282][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-11-02 08:48:39.284][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.289][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.294][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.300][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-11-02 08:48:39.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:39.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:39.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:39.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:39.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:39.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:39.316][FUN] Functions in observer BiodbConfig: [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[2023-11-02 08:48:39.317][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.322][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.328][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:48:39.329][private$selectFields]
biodb.TRACE[2023-11-02 08:48:39.331][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:48:39.333][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:48:39.334][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:48:39.335][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.337][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.338][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.339][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.341][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.342][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.343][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.345][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.346][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:48:39.347][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:48:39.349][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.350][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.351][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.353][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.354][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-11-02 08:48:39.355][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.361][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.366][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:48:39.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.389][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-11-02 08:48:39.391][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-11-02 08:48:39.392][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-11-02 08:48:39.406][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-11-02 08:48:39.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-11-02 08:48:39.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-11-02 08:48:39.418][biodb::testThat]
biodb.INFO [2023-11-02 08:48:39.419][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-11-02 08:48:39.421][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:48:39.422][biodb::testThat]
biodb.TRACE[2023-11-02 08:48:39.426][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-11-02 08:48:39.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-11-02 08:48:39.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:48:39.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:48:39.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:39.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:39.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:39.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:39.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:39.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:39.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:48:39.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:39.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:48:39.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:48:39.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:48:39.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:48:39.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:48:39.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:48:39.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:48:39.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:48:39.548][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:48:39.549][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[2023-11-02 08:48:39.554][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[2023-11-02 08:48:39.558][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:48:39.559][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:48:39.562][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2023-11-02 08:48:44.514][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2023-11-02 08:49:05.026][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:49:05.029][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2023-11-02 08:49:05.061][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2023-11-02 08:49:06.251][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-11-02 08:49:06.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:49:06.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:49:06.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:49:06.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:49:06.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:49:06.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:49:06.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:49:06.319][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.325][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.360][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:06.362][private$selectFields]
biodb.TRACE[2023-11-02 08:49:06.363][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:49:06.364][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:49:06.366][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:06.367][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.369][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.370][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.371][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.373][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.374][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.375][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.377][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.378][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:06.416][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:06.418][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.419][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.420][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.422][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.423][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-11-02 08:49:06.424][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.430][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.435][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.441][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-11-02 08:49:06.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:49:06.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:49:06.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:49:06.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:49:06.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:49:06.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:49:06.458][FUN] Functions in observer BiodbConfig: [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[2023-11-02 08:49:06.460][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.465][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.471][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:06.472][private$selectFields]
biodb.TRACE[2023-11-02 08:49:06.473][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:49:06.475][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:49:06.476][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:06.477][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.479][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.481][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.483][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.484][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.485][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.487][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.488][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:06.489][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:06.491][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.492][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.493][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.495][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.496][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-11-02 08:49:06.497][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.503][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.508][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.514][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-11-02 08:49:06.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:49:06.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:49:06.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:49:06.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:49:06.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:49:06.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:49:06.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:49:06.533][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.538][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.544][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:06.545][private$selectFields]
biodb.TRACE[2023-11-02 08:49:06.546][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:49:06.548][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:49:06.549][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:06.550][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.552][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.553][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.555][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.556][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.557][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.559][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.560][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.561][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:06.563][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:06.564][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.565][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.567][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.568][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.569][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-11-02 08:49:06.571][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.576][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.582][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:06.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.588][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-11-02 08:49:06.590][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-11-02 08:49:06.591][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-11-02 08:49:06.605][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-11-02 08:49:06.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-11-02 08:49:06.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-11-02 08:49:06.617][biodb::testThat]
biodb.INFO [2023-11-02 08:49:06.618][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-11-02 08:49:06.620][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:49:06.621][biodb::testThat]
biodb.TRACE[2023-11-02 08:49:06.643][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-11-02 08:49:06.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-11-02 08:49:06.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-11-02 08:49:06.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-11-02 08:49:06.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:49:06.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:49:06.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:49:06.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:49:06.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:49:06.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:49:06.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:06.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:49:06.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:49:06.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:06.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:49:06.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:49:06.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:49:06.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:49:06.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:49:06.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:49:06.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:49:06.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:49:06.704][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-11-02 08:49:06.709][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:49:06.711][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-11-02 08:49:06.713][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:49:06.805][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-11-02 08:49:08.231][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-11-02 08:49:08.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:49:08.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:49:08.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:49:08.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:49:08.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:49:08.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:49:08.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:49:08.253][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.259][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.265][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:08.266][private$selectFields]
biodb.TRACE[2023-11-02 08:49:08.268][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:49:08.269][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:49:08.270][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:08.272][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.274][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.275][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.277][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.278][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.279][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.281][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.282][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.284][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:08.285][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:08.286][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.288][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.289][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.290][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.292][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-11-02 08:49:08.293][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.299][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.304][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.310][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-11-02 08:49:08.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:49:08.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:49:08.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:49:08.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:49:08.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:49:08.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:49:08.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:49:08.329][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.335][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.341][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:08.342][private$selectFields]
biodb.TRACE[2023-11-02 08:49:08.343][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:49:08.345][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:49:08.346][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:08.347][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.349][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.350][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.352][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.353][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.355][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.356][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.358][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.360][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:08.362][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:08.363][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.365][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.366][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.367][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.369][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-11-02 08:49:08.370][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.376][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.382][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.389][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-11-02 08:49:08.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:49:08.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:49:08.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:49:08.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:49:08.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:49:08.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:49:08.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:49:08.409][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.415][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.422][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:08.423][private$selectFields]
biodb.TRACE[2023-11-02 08:49:08.425][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-11-02 08:49:08.426][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:49:08.428][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:08.429][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.431][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.432][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.434][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.435][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.437][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.439][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.440][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.441][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:08.443][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:49:08.445][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.446][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.448][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.449][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.451][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-11-02 08:49:08.452][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.457][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.463][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:08.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:08.469][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-11-02 08:49:08.470][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-11-02 08:49:08.471][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-11-02 08:49:08.504][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-11-02 08:49:08.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-11-02 08:49:08.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:08.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-11-02 08:49:08.516][biodb::testThat]
biodb.INFO [2023-11-02 08:49:08.517][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-11-02 08:49:08.518][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:49:08.520][biodb::testThat]
biodb.DEBUG[2023-11-02 08:49:08.522][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-11-02 08:49:08.524][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-11-02 08:49:08.526][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-11-02 08:49:08.527][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-11-02 08:49:08.529][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:49:08.530][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:49:08.532][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-11-02 08:49:08.533][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:49:08.534][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:49:08.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:49:08.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:49:08.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:49:08.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:49:08.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:49:08.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:49:08.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:49:08.572][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-11-02 08:49:08.576][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:08.578][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:08.580][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-11-02 08:49:09.834][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:09.835][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:09.837][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-11-02 08:49:09.838][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-11-02 08:49:11.136][private$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[2023-11-02 08:49:11.138][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:11.140][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:11.142][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-11-02 08:49:12.336][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:12.337][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:12.338][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-11-02 08:49:12.340][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-11-02 08:49:13.645][private$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[2023-11-02 08:49:13.646][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:13.648][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:13.650][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-11-02 08:49:14.859][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:14.861][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:14.862][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-11-02 08:49:14.864][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-11-02 08:49:20.178][private$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[2023-11-02 08:49:20.179][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:20.181][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:20.182][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-11-02 08:49:21.360][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:21.361][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:21.363][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-11-02 08:49:21.365][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-11-02 08:49:22.680][private$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[2023-11-02 08:49:22.682][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:22.683][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:22.685][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-11-02 08:49:23.886][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:23.888][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:23.889][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-11-02 08:49:23.891][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-11-02 08:49:25.196][private$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[2023-11-02 08:49:25.197][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:25.199][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:25.239][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-11-02 08:49:26.444][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:26.445][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:26.446][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-11-02 08:49:26.448][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-11-02 08:49:27.747][private$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[2023-11-02 08:49:27.749][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:27.750][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:27.752][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-11-02 08:49:28.919][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:28.920][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:28.921][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-11-02 08:49:28.922][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-11-02 08:49:30.229][private$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[2023-11-02 08:49:30.230][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:30.232][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:30.233][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-11-02 08:49:31.415][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:31.416][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:31.418][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-11-02 08:49:31.419][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-11-02 08:49:32.719][private$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[2023-11-02 08:49:32.720][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:32.722][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:32.724][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-11-02 08:49:33.909][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:33.911][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:33.913][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-11-02 08:49:33.914][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-11-02 08:49:35.231][private$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[2023-11-02 08:49:35.232][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:35.234][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:35.236][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-11-02 08:49:36.414][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:36.415][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:36.417][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-11-02 08:49:36.418][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-11-02 08:49:37.720][private$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[2023-11-02 08:49:37.724][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-11-02 08:49:37.726][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:49:37.728][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-11-02 08:49:37.730][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-11-02 08:49:37.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:49:37.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:49:37.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:49:37.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:49:37.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:49:37.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:49:37.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:49:37.753][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:37.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:37.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:37.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:37.758][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:37.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:49:37.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:37.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:37.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:49:37.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:49:37.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:37.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:37.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:49:37.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:49:37.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:37.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:37.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:49:37.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:49:37.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:37.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:37.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:49:37.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:49:37.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:37.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:37.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:49:37.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:49:37.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:37.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:49:37.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:49:37.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:49:37.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:49:37.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:49:37.802][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-11-02 08:49:37.804][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-11-02 08:49:37.820][biodb::testThat]
biodb.INFO [2023-11-02 08:49:37.821][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-11-02 08:49:37.823][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:49:37.824][biodb::testThat]
biodb.DEBUG[2023-11-02 08:49:37.838][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-11-02 08:49:37.839][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-11-02 08:49:37.841][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-11-02 08:49:37.843][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-11-02 08:49:37.845][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-11-02 08:49:37.847][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-11-02 08:49:37.848][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:49:37.850][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-11-02 08:49:37.852][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-11-02 08:49:37.853][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-11-02 08:49:37.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:49:37.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:49:37.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:49:37.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:49:37.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:49:37.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:49:37.876][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.DEBUG[2023-11-02 08:49:37.877][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-11-02 08:49:37.881][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:37.883][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:37.885][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-11-02 08:49:39.064][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:39.066][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:39.067][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[2023-11-02 08:49:39.069][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-11-02 08:49:40.370][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-11-02 08:49:40.371][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:40.373][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:40.375][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-11-02 08:49:41.564][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:41.566][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:41.567][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-11-02 08:49:41.569][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-11-02 08:49:42.880][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-11-02 08:49:42.882][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:42.883][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:42.885][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-11-02 08:49:44.072][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:44.074][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:44.076][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[2023-11-02 08:49:44.077][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-11-02 08:49:45.376][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-11-02 08:49:45.378][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:45.379][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:45.381][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-11-02 08:49:46.565][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:46.566][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:46.568][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[2023-11-02 08:49:46.569][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-11-02 08:49:47.879][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-11-02 08:49:47.881][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:47.882][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:47.884][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-11-02 08:49:49.052][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:49.053][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:49.054][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[2023-11-02 08:49:49.056][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-11-02 08:49:50.364][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-11-02 08:49:50.366][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:50.367][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:50.369][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-11-02 08:49:51.549][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:51.550][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:51.552][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[2023-11-02 08:49:51.553][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-11-02 08:49:52.851][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-11-02 08:49:52.852][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:52.854][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:52.856][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-11-02 08:49:54.052][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:54.054][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:54.056][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[2023-11-02 08:49:54.057][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-11-02 08:49:55.359][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-11-02 08:49:55.361][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:55.362][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:55.364][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-11-02 08:49:56.528][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:56.529][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:56.531][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[2023-11-02 08:49:56.533][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-11-02 08:49:57.840][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-11-02 08:49:57.842][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:49:57.844][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:49:57.846][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-11-02 08:49:59.031][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:49:59.032][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:49:59.034][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[2023-11-02 08:49:59.035][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-11-02 08:50:00.336][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-11-02 08:50:00.337][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:50:00.338][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:50:00.340][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-11-02 08:50:01.530][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-11-02 08:50:01.531][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-11-02 08:50:01.533][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[2023-11-02 08:50:01.535][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-11-02 08:50:02.835][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-11-02 08:50:02.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:50:02.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:02.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:02.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:02.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:02.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:02.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:02.856][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-11-02 08:50:02.860][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:50:02.861][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:50:02.863][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-11-02 08:50:04.116][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-11-02 08:50:05.341][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:50:05.346][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-11-02 08:50:05.352][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-11-02 08:50:05.356][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2023-11-02 08:50:05.358][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-11-02 08:50:05.360][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-11-02 08:50:05.362][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-11-02 08:50:05.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:50:05.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:05.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:05.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:05.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:05.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:05.382][FUN] Functions in observer BiodbConfig: [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[2023-11-02 08:50:05.385][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:05.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:05.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.391][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:05.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:05.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:50:05.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:50:05.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:05.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:05.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:05.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:05.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:05.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:50:05.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:05.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:05.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:05.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:05.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.538][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:50:05.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:50:05.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.544][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:50:05.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:50:05.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.550][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:50:05.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:50:05.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.555][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:50:05.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:50:05.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.561][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:05.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:05.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.567][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:05.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:05.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.572][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:05.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:05.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.578][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:05.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:05.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.585][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:50:05.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:05.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.590][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:50:05.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:05.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.596][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:05.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:05.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.602][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:05.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:05.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:05.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:05.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:05.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:05.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.619][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:50:05.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:05.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.624][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-11-02 08:50:05.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:05.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:05.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:05.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:05.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:05.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.642][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:50:05.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:05.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:05.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:05.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:05.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:05.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:05.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:05.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:05.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:05.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:05.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:05.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.676][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:05.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:05.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.682][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:05.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:05.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.693][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:05.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:05.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:05.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:05.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:05.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:05.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:50:05.758][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-11-02 08:50:05.760][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-11-02 08:50:05.761][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-11-02 08:50:05.784][biodb::testThat]
biodb.INFO [2023-11-02 08:50:05.785][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-11-02 08:50:05.787][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:50:05.788][biodb::testThat]
biodb.INFO [2023-11-02 08:50:05.825][biodb::testThat]
biodb.INFO [2023-11-02 08:50:05.827][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-11-02 08:50:05.828][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:50:05.830][biodb::testThat]
biodb.INFO [2023-11-02 08:50:05.846][biodb::testThat]
biodb.INFO [2023-11-02 08:50:05.847][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-11-02 08:50:05.848][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:50:05.850][biodb::testThat]
biodb.DEBUG[2023-11-02 08:50:05.854][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[2023-11-02 08:50:05.859][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:50:05.860][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:50:05.862][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-11-02 08:50:10.319][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-11-02 08:50:20.428][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:50:20.433][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-11-02 08:50:20.468][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-11-02 08:50:21.605][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:21.606][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:21.608][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:21.609][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:21.610][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:21.612][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:21.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:21.614][ef$get] fields variable is a list.
biodb.INFO [2023-11-02 08:50:21.617][biodb::testThat]
biodb.INFO [2023-11-02 08:50:21.618][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-11-02 08:50:21.619][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:50:21.621][biodb::testThat]
biodb.ERROR[2023-11-02 08:50:21.643][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-11-02 08:50:21.669][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-11-02 08:50:21.691][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-11-02 08:50:21.693][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-11-02 08:50:21.694][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-11-02 08:50:21.695][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-11-02 08:50:21.697][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:21.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:21.699][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:21.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:21.702][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-11-02 08:50:21.718][biodb::testContext]
biodb.INFO [2023-11-02 08:50:21.720][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:50:21.721][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-11-02 08:50:21.722][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:50:21.724][biodb::testContext]
biodb.INFO [2023-11-02 08:50:21.727][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:50:21.730][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-11-02 08:50:21.736][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:50:21.737][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-11-02 08:50:21.739][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-11-02 08:50:21.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.745][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-11-02 08:50:21.746][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-11-02 08:50:21.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.752][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-11-02 08:50:21.753][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-11-02 08:50:21.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.759][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-11-02 08:50:21.760][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-11-02 08:50:21.762][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-11-02 08:50:21.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.767][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-11-02 08:50:21.769][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-11-02 08:50:21.771][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-11-02 08:50:21.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.776][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-11-02 08:50:21.778][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-11-02 08:50:21.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.783][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-11-02 08:50:21.785][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-11-02 08:50:21.787][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-11-02 08:50:21.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.792][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-11-02 08:50:21.794][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-11-02 08:50:21.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.800][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-11-02 08:50:21.801][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-11-02 08:50:21.803][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-11-02 08:50:21.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.807][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.DEBUG[2023-11-02 08:50:21.808][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:50:21.810][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-11-02 08:50:21.811][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-11-02 08:50:21.812][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-11-02 08:50:21.814][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-11-02 08:50:21.815][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-11-02 08:50:21.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.821][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-11-02 08:50:21.822][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-11-02 08:50:21.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.827][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-11-02 08:50:21.829][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-11-02 08:50:21.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.834][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-11-02 08:50:21.836][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-11-02 08:50:21.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.841][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-11-02 08:50:21.842][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-11-02 08:50:21.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.847][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-11-02 08:50:21.849][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-11-02 08:50:21.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.854][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:50:21.855][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-11-02 08:50:21.860][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-11-02 08:50:21.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.865][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-11-02 08:50:21.867][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-11-02 08:50:21.868][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-11-02 08:50:21.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:21.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:21.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:21.875][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-11-02 08:50:21.878][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:21.879][self$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[2023-11-02 08:50:21.880][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:21.882][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:50:21.883][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:21.885][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:50:21.888][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:21.889][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:50:21.890][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:50:21.892][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:50:21.893][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:21.895][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-11-02 08:50:21.896][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:50:21.898][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:21.899][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:21.900][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:50:21.900][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:50:21.900][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:50:21.900][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:50:21.900][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:50:21.902][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:50:21.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:21.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:21.906][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:50:21.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:21.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:21.910][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:50:21.911][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:21.913][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:50:21.914][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:50:21.915][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:21.917][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:21.919][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-11-02 08:50:21.921][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:21.923][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:50:21.924][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:21.926][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:50:21.927][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:21.929][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:50:21.930][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:21.932][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:50:21.933][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:50:21.934][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:50:21.936][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:21.937][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-11-02 08:50:21.939][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:50:21.940][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:21.942][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:21.943][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:50:21.943][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:50:21.943][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:50:21.943][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:50:21.943][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:50:21.945][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:50:21.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:21.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:21.949][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:50:21.950][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:21.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:21.953][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:50:21.954][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:21.956][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:50:21.957][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:50:21.959][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:21.960][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:21.962][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-11-02 08:50:21.964][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:21.966][self$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[2023-11-02 08:50:21.967][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:21.969][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:50:21.970][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:21.971][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:50:21.973][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:21.974][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:50:21.976][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:50:21.977][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:50:21.979][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:21.980][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-11-02 08:50:21.981][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:50:21.983][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:21.984][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:21.986][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:21.987][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:50:21.989][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:21.990][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:21.991][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:50:21.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:21.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:21.995][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:50:21.997][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:21.999][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:50:22.000][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:50:22.002][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:22.003][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:22.005][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-11-02 08:50:22.007][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:22.009][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:50:22.011][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:22.012][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:50:22.014][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:22.049][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:50:22.051][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:22.052][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:50:22.053][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:50:22.055][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:50:22.056][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:22.058][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-11-02 08:50:22.059][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:50:22.060][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:22.062][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:22.063][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:22.064][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:50:22.066][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:22.067][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:22.068][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:50:22.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:22.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:22.072][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:50:22.074][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:22.075][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:50:22.077][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:50:22.079][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:22.080][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:22.082][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:50:22.083][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.116][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[2023-11-02 08:50:22.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.194][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-11-02 08:50:22.196][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-11-02 08:50:22.198][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-11-02 08:50:22.201][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-11-02 08:50:22.203][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-11-02 08:50:22.205][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-11-02 08:50:22.207][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-11-02 08:50:22.209][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-11-02 08:50:22.211][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-11-02 08:50:22.213][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-11-02 08:50:22.215][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-11-02 08:50:22.217][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-11-02 08:50:22.219][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-11-02 08:50:22.221][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-11-02 08:50:22.223][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-11-02 08:50:22.225][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-11-02 08:50:22.227][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-11-02 08:50:22.229][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-11-02 08:50:22.232][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-11-02 08:50:22.234][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-11-02 08:50:22.236][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-11-02 08:50:22.238][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-11-02 08:50:22.240][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-11-02 08:50:22.242][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-11-02 08:50:22.244][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-11-02 08:50:22.246][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-11-02 08:50:22.248][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-11-02 08:50:22.250][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-11-02 08:50:22.252][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-11-02 08:50:22.254][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-11-02 08:50:22.256][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-11-02 08:50:22.258][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-11-02 08:50:22.260][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-11-02 08:50:22.262][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-11-02 08:50:22.264][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-11-02 08:50:22.266][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-11-02 08:50:22.268][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-11-02 08:50:22.270][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-11-02 08:50:22.272][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-11-02 08:50:22.274][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-11-02 08:50:22.276][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-11-02 08:50:22.278][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-11-02 08:50:22.281][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-11-02 08:50:22.284][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-11-02 08:50:22.286][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-11-02 08:50:22.288][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-11-02 08:50:22.290][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-11-02 08:50:22.292][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-11-02 08:50:22.294][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-11-02 08:50:22.296][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-11-02 08:50:22.298][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-11-02 08:50:22.300][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-11-02 08:50:22.302][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-11-02 08:50:22.304][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-11-02 08:50:22.306][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-11-02 08:50:22.308][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-11-02 08:50:22.310][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-11-02 08:50:22.312][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-11-02 08:50:22.314][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-11-02 08:50:22.316][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-11-02 08:50:22.318][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-11-02 08:50:22.320][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-11-02 08:50:22.322][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-11-02 08:50:22.324][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-11-02 08:50:22.326][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-11-02 08:50:22.328][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-11-02 08:50:22.330][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-11-02 08:50:22.332][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-11-02 08:50:22.334][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-11-02 08:50:22.336][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-11-02 08:50:22.338][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-11-02 08:50:22.340][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-11-02 08:50:22.342][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-11-02 08:50:22.344][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-11-02 08:50:22.346][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-11-02 08:50:22.348][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-11-02 08:50:22.350][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-11-02 08:50:22.352][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-11-02 08:50:22.354][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-11-02 08:50:22.356][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-11-02 08:50:22.358][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-11-02 08:50:22.360][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-11-02 08:50:22.362][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-11-02 08:50:22.364][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-11-02 08:50:22.367][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:50:22.368][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:50:22.369][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.372][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.486][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[2023-11-02 08:50:22.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.513][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[2023-11-02 08:50:22.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:22.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:22.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:22.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:22.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:22.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:22.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:22.555][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-11-02 08:50:22.558][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-11-02 08:50:22.560][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:22.562][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-11-02 08:50:22.564][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:22.565][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:50:22.566][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:22.568][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:50:22.569][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:22.571][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:50:22.572][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:50:22.574][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:50:22.575][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:22.577][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-11-02 08:50:22.578][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:50:22.580][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-11-02 08:50:22.580][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-11-02 08:50:22.580][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-11-02 08:50:22.580][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-11-02 08:50:22.580][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-11-02 08:50:22.580][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-11-02 08:50:22.580][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-11-02 08:50:22.580][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-11-02 08:50:22.580][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-11-02 08:50:22.581][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:22.583][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:50:22.583][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:50:22.584][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:50:22.586][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:22.587][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:22.589][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:50:22.590][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:22.591][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:22.593][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:50:22.594][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-11-02 08:50:22.594][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-11-02 08:50:22.596][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:50:22.597][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:50:22.599][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:22.600][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:22.602][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-11-02 08:50:22.604][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-11-02 08:50:22.609][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-11-02 08:50:22.610][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-11-02 08:50:22.612][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-11-02 08:50:22.614][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-11-02 08:50:22.616][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-11-02 08:50:22.617][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-11-02 08:50:22.619][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-11-02 08:50:22.620][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-11-02 08:50:22.622][biodb::testThat]
biodb.INFO [2023-11-02 08:50:22.624][biodb::testThat] Running test function  test_wsLmsdRecord_searchByName  (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-11-02 08:50:22.625][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:50:22.626][biodb::testThat]
biodb.DEBUG[2023-11-02 08:50:22.632][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2023-11-02 08:50:22.638][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:50:22.640][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:50:22.642][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-11-02 08:50:23.856][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[2023-11-02 08:50:25.059][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:50:25.062][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-11-02 08:50:25.067][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-11-02 08:50:25.081][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[2023-11-02 08:50:25.085][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:50:25.087][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:50:25.089][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-11-02 08:50:26.318][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2023-11-02 08:50:27.533][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:50:27.536][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-11-02 08:50:27.541][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-11-02 08:50:27.560][biodb::testThat]
biodb.INFO [2023-11-02 08:50:27.561][biodb::testThat] Running test function  test_wsLmsdRecord  (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-11-02 08:50:27.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:50:27.564][biodb::testThat]
biodb.INFO [2023-11-02 08:50:27.610][biodb::testThat]
biodb.INFO [2023-11-02 08:50:27.612][biodb::testThat] Running test function  test_wsLmsdSearch  (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-11-02 08:50:27.613][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:50:27.615][biodb::testThat]
biodb.DEBUG[2023-11-02 08:50:27.620][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-11-02 08:50:27.624][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:50:27.626][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:50:27.629][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-11-02 08:50:28.677][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-11-02 08:50:29.748][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:50:29.751][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-11-02 08:50:29.757][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-11-02 08:50:29.765][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[2023-11-02 08:50:29.769][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:50:29.771][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-11-02 08:50:29.773][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:50:29.775][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-11-02 08:50:29.784][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[2023-11-02 08:50:29.788][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:50:29.790][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:50:29.792][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-11-02 08:50:30.838][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2023-11-02 08:50:32.009][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:50:32.025][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-11-02 08:50:32.033][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-11-02 08:50:32.048][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2023-11-02 08:50:32.052][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:50:32.054][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:50:32.056][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-11-02 08:50:35.371][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-11-02 08:50:38.220][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:50:38.223][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-11-02 08:50:38.232][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-11-02 08:50:38.388][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[2023-11-02 08:50:38.393][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-11-02 08:50:38.394][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-11-02 08:50:38.397][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2023-11-02 08:50:40.198][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2023-11-02 08:50:43.069][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-11-02 08:50:43.072][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-11-02 08:50:43.080][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-11-02 08:50:43.239][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-11-02 08:50:43.241][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-11-02 08:50:43.243][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-11-02 08:50:43.244][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-11-02 08:50:43.245][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:43.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:43.248][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.251][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-11-02 08:50:43.265][biodb::testContext]
biodb.INFO [2023-11-02 08:50:43.266][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:50:43.268][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-11-02 08:50:43.269][biodb::testContext] ********************************************************************************
biodb.INFO [2023-11-02 08:50:43.270][biodb::testContext]
biodb.INFO [2023-11-02 08:50:43.275][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:50:43.281][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-11-02 08:50:43.287][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:50:43.288][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-11-02 08:50:43.290][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-11-02 08:50:43.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.296][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-11-02 08:50:43.297][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-11-02 08:50:43.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.303][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-11-02 08:50:43.304][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-11-02 08:50:43.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.310][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-11-02 08:50:43.311][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-11-02 08:50:43.313][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-11-02 08:50:43.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.318][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-11-02 08:50:43.320][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-11-02 08:50:43.322][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-11-02 08:50:43.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.327][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-11-02 08:50:43.329][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-11-02 08:50:43.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.334][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-11-02 08:50:43.336][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-11-02 08:50:43.338][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-11-02 08:50:43.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.343][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-11-02 08:50:43.345][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-11-02 08:50:43.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.350][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-11-02 08:50:43.352][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-11-02 08:50:43.354][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-11-02 08:50:43.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.359][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:50:43.361][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-11-02 08:50:43.362][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-11-02 08:50:43.364][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-11-02 08:50:43.365][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-11-02 08:50:43.367][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-11-02 08:50:43.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.372][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-11-02 08:50:43.374][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-11-02 08:50:43.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.378][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[2023-11-02 08:50:43.380][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-11-02 08:50:43.381][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-11-02 08:50:43.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.387][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-11-02 08:50:43.388][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-11-02 08:50:43.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.394][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-11-02 08:50:43.395][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-11-02 08:50:43.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.401][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-11-02 08:50:43.402][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-11-02 08:50:43.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.408][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-11-02 08:50:43.409][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-11-02 08:50:43.414][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-11-02 08:50:43.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.420][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-11-02 08:50:43.422][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-11-02 08:50:43.423][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-11-02 08:50:43.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.429][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-11-02 08:50:43.432][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:43.433][self$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[2023-11-02 08:50:43.435][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.436][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:50:43.438][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.439][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:50:43.441][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:43.442][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:50:43.444][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:50:43.445][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:50:43.447][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.448][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-11-02 08:50:43.450][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:50:43.451][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.453][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.454][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:50:43.454][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:50:43.454][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:50:43.454][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:50:43.454][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:50:43.456][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:50:43.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:43.460][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:43.461][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:50:43.463][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:43.464][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:43.466][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:50:43.467][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.469][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:50:43.470][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:50:43.471][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:43.473][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.475][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-11-02 08:50:43.478][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:43.479][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:50:43.481][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.483][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:50:43.484][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.486][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:50:43.488][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:43.489][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:50:43.491][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:50:43.493][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:50:43.494][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.496][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-11-02 08:50:43.497][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:50:43.499][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.501][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.502][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:50:43.502][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:50:43.502][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-11-02 08:50:43.502][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-11-02 08:50:43.502][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-11-02 08:50:43.504][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:50:43.506][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:43.507][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:43.509][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:50:43.510][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:43.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:43.513][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:50:43.515][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.517][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:50:43.518][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:50:43.520][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:43.521][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.523][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-11-02 08:50:43.526][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.527][self$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[2023-11-02 08:50:43.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.530][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:50:43.532][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.533][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:50:43.534][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:43.536][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:50:43.537][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:50:43.539][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:50:43.540][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:43.542][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-11-02 08:50:43.543][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:50:43.545][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.546][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.548][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.549][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:50:43.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:43.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:43.553][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:50:43.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:43.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:43.558][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:50:43.559][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.561][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:50:43.562][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:50:43.563][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:43.565][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.567][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-11-02 08:50:43.569][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.571][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-11-02 08:50:43.572][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.574][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:50:43.575][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.577][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:50:43.578][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:43.580][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:50:43.581][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-11-02 08:50:43.583][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:50:43.584][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:43.586][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-11-02 08:50:43.587][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:50:43.589][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.590][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:43.592][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.593][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:50:43.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:43.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:43.598][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:50:43.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:43.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:43.602][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:50:43.604][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:50:43.607][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:50:43.608][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:43.610][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:43.612][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:50:43.613][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.648][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[2023-11-02 08:50:43.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.688][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[2023-11-02 08:50:43.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.706][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[2023-11-02 08:50:43.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.724][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[2023-11-02 08:50:43.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.744][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-11-02 08:50:43.746][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-11-02 08:50:43.748][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-11-02 08:50:43.750][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-11-02 08:50:43.752][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-11-02 08:50:43.754][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-11-02 08:50:43.756][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-11-02 08:50:43.757][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-11-02 08:50:43.759][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-11-02 08:50:43.761][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-11-02 08:50:43.763][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-11-02 08:50:43.765][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-11-02 08:50:43.768][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-11-02 08:50:43.770][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-11-02 08:50:43.772][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-11-02 08:50:43.774][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-11-02 08:50:43.776][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-11-02 08:50:43.778][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-11-02 08:50:43.780][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-11-02 08:50:43.782][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-11-02 08:50:43.784][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-11-02 08:50:43.786][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-11-02 08:50:43.788][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-11-02 08:50:43.790][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-11-02 08:50:43.792][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-11-02 08:50:43.794][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-11-02 08:50:43.796][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-11-02 08:50:43.798][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-11-02 08:50:43.800][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-11-02 08:50:43.802][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-11-02 08:50:43.804][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-11-02 08:50:43.806][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-11-02 08:50:43.808][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-11-02 08:50:43.810][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-11-02 08:50:43.812][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-11-02 08:50:43.814][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-11-02 08:50:43.816][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-11-02 08:50:43.818][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-11-02 08:50:43.820][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-11-02 08:50:43.822][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-11-02 08:50:43.824][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-11-02 08:50:43.826][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-11-02 08:50:43.828][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-11-02 08:50:43.830][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-11-02 08:50:43.832][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-11-02 08:50:43.834][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-11-02 08:50:43.837][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-11-02 08:50:43.839][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-11-02 08:50:43.841][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-11-02 08:50:43.843][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-11-02 08:50:43.845][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-11-02 08:50:43.847][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-11-02 08:50:43.849][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-11-02 08:50:43.851][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-11-02 08:50:43.853][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-11-02 08:50:43.855][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-11-02 08:50:43.857][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-11-02 08:50:43.859][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-11-02 08:50:43.861][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-11-02 08:50:43.863][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-11-02 08:50:43.866][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-11-02 08:50:43.868][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-11-02 08:50:43.870][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-11-02 08:50:43.872][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-11-02 08:50:43.874][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-11-02 08:50:43.876][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-11-02 08:50:43.878][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-11-02 08:50:43.880][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-11-02 08:50:43.882][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-11-02 08:50:43.884][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-11-02 08:50:43.886][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-11-02 08:50:43.888][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-11-02 08:50:43.890][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-11-02 08:50:43.892][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-11-02 08:50:43.894][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-11-02 08:50:43.896][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-11-02 08:50:43.898][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-11-02 08:50:43.900][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-11-02 08:50:43.902][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-11-02 08:50:43.904][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-11-02 08:50:43.907][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-11-02 08:50:43.909][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-11-02 08:50:43.911][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-11-02 08:50:43.913][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-11-02 08:50:43.915][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2023-11-02 08:50:43.917][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-11-02 08:50:43.918][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.920][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:43.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:43.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.931][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[2023-11-02 08:50:43.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:43.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:43.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.940][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[2023-11-02 08:50:43.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:43.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:43.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:43.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:43.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:43.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:43.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:43.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:43.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:43.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:43.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:43.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:43.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:43.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:43.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:43.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:43.993][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[2023-11-02 08:50:43.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:43.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:43.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:43.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:44.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:44.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:44.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:44.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:44.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:44.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:44.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:44.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:44.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:44.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:44.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:44.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:44.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:44.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:44.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:44.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:44.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:44.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:44.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:44.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:44.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:44.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:44.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:44.029][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.DEBUG[2023-11-02 08:50:44.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:44.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:44.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:44.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:44.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:44.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:44.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:44.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:44.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:44.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:44.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:44.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:44.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:44.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:44.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:44.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:44.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:44.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:44.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:44.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:44.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:44.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:44.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:44.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:44.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:44.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:44.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:44.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:44.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-11-02 08:50:44.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:44.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:44.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:44.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:44.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:44.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-11-02 08:50:44.099][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.1/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-11-02 08:50:44.102][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-11-02 08:50:44.104][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:44.106][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-11-02 08:50:44.108][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:44.109][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-11-02 08:50:44.111][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:44.112][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-11-02 08:50:44.114][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:44.115][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-11-02 08:50:44.117][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-11-02 08:50:44.118][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-11-02 08:50:44.120][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:44.121][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-11-02 08:50:44.123][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-11-02 08:50:44.124][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-11-02 08:50:44.124][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-11-02 08:50:44.124][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-11-02 08:50:44.124][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-11-02 08:50:44.124][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-11-02 08:50:44.124][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-11-02 08:50:44.124][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-11-02 08:50:44.124][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-11-02 08:50:44.124][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-11-02 08:50:44.126][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-11-02 08:50:44.127][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-11-02 08:50:44.127][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-11-02 08:50:44.129][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-11-02 08:50:44.130][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:44.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:44.133][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-11-02 08:50:44.135][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-11-02 08:50:44.136][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-11-02 08:50:44.138][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-11-02 08:50:44.139][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-11-02 08:50:44.139][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-11-02 08:50:44.141][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-11-02 08:50:44.142][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-11-02 08:50:44.144][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-11-02 08:50:44.145][self$setPropertyValue]
biodb.DEBUG[2023-11-02 08:50:44.147][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-11-02 08:50:44.150][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-11-02 08:50:44.154][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-11-02 08:50:44.156][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-11-02 08:50:44.158][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-11-02 08:50:44.160][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-11-02 08:50:44.162][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-11-02 08:50:44.163][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-11-02 08:50:44.165][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-11-02 08:50:44.167][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-11-02 08:50:44.169][biodb::testThat]
biodb.INFO [2023-11-02 08:50:44.170][biodb::testThat] Running test function  test_noOtherConnNeeded  (" No other connector is needed. ").
biodb.INFO [2023-11-02 08:50:44.172][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-11-02 08:50:44.173][biodb::testThat]
biodb.DEBUG[2023-11-02 08:50:44.179][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-11-02 08:50:44.185][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-11-02 08:50:44.187][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-11-02 08:50:44.189][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-11-02 08:50:44.307][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-11-02 08:50:45.424][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-11-02 08:50:45.426][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-11-02 08:50:45.432][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-11-02 08:50:45.435][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-11-02 08:50:45.439][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2023-11-02 08:50:45.440][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-11-02 08:50:45.442][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-11-02 08:50:45.444][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-11-02 08:50:45.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:50:45.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:45.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:45.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:45.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:45.460][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:45.461][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.TRACE[2023-11-02 08:50:45.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:45.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:45.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:45.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:45.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.491][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:50:45.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:50:45.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.498][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:50:45.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:50:45.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.504][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:45.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:45.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.510][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:45.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:45.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.516][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:45.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:45.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.521][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:45.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:45.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.527][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:50:45.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:45.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.533][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:50:45.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:45.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.539][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:45.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:45.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.545][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:45.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:45.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.562][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:50:45.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.568][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-11-02 08:50:45.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.585][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:50:45.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.597][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.603][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.620][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:45.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:45.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.626][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:45.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:45.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.638][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:45.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:45.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:50:45.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:50:45.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:45.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:45.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:45.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:45.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:45.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:50:45.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:45.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:45.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:45.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:45.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.710][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:50:45.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-11-02 08:50:45.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.716][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:50:45.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-11-02 08:50:45.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.722][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:45.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:45.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.728][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:45.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:45.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.734][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:45.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:45.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.740][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:45.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:45.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.746][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:50:45.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:45.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.752][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-11-02 08:50:45.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:45.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.758][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:45.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:45.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.764][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:45.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:45.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.783][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:50:45.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.789][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-11-02 08:50:45.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:45.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.807][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-11-02 08:50:45.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:45.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.813][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:45.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:45.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.819][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:45.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:45.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.831][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:45.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:45.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-11-02 08:50:45.916][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-11-02 08:50:45.922][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-11-02 08:50:45.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:50:45.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:45.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:45.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:45.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:45.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:45.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:50:45.943][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:50:45.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:50:45.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.949][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:50:45.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:50:45.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.956][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-11-02 08:50:45.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-11-02 08:50:45.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.962][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-11-02 08:50:45.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-11-02 08:50:45.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.968][private$selectFields] Fields none
biodb.TRACE[2023-11-02 08:50:45.969][private$selectFields]
biodb.TRACE[2023-11-02 08:50:45.971][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-11-02 08:50:45.972][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:50:45.974][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:50:45.975][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:45.977][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:45.978][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.980][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.981][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:45.983][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:45.984][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.986][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.987][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:45.989][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:45.990][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.992][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.993][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:45.995][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:45.996][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:45.998][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:45.999][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.001][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.004][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.005][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:46.007][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:46.008][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.010][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.011][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:46.013][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:46.014][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.016][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.017][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.019][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.021][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.022][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.024][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:46.025][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:46.027][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.028][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.030][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.032][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.033][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.035][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.036][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.038][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.039][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.041][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.042][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.044][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.046][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.047][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.049][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.050][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.052][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.053][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.055][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:46.057][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:46.058][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.060][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.061][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:46.063][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:46.065][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.066][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.068][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.069][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.071][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.072][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.074][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:50:46.075][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:50:46.077][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:46.079][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:46.080][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.082][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.083][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.085][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.086][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.088][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.089][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.091][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.093][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.094][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.096][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.097][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.099][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.101][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.103][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.105][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.107][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.108][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.110][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:46.112][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:46.113][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.115][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.116][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:46.118][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:46.120][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.121][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.123][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.125][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.126][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.128][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.129][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-11-02 08:50:46.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:46.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:46.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:46.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:46.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:46.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:46.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.168][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.173][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.179][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.185][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.191][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.197][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.221][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:46.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:46.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.227][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:46.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:46.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.232][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:46.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:46.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.238][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:46.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:46.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:46.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:46.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:46.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:46.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.256][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.262][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.268][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.282][private$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[2023-11-02 08:50:46.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-11-02 08:50:46.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:46.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:46.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:46.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:46.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:46.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-11-02 08:50:46.322][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:50:46.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:50:46.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.327][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-11-02 08:50:46.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-11-02 08:50:46.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.333][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-11-02 08:50:46.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-11-02 08:50:46.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.338][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-11-02 08:50:46.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-11-02 08:50:46.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.344][private$selectFields] Fields none
biodb.TRACE[2023-11-02 08:50:46.345][private$selectFields]
biodb.TRACE[2023-11-02 08:50:46.346][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-11-02 08:50:46.348][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-11-02 08:50:46.349][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:50:46.350][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:46.352][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:46.353][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.354][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.356][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.357][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.359][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.360][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.361][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.363][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.364][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.365][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.367][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.368][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.369][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.371][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.372][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.374][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.375][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.376][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.378][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:46.379][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:46.380][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.382][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.383][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:46.385][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:46.386][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.387][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.389][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.390][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.391][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.393][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.394][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:46.395][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:46.397][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.398][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.399][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.401][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.402][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.403][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.405][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.406][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.408][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.409][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.410][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.412][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.413][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.414][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.416][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.417][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.419][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.420][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.421][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:46.423][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:46.424][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.426][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.427][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:46.429][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:46.430][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.432][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.433][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.435][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.436][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.437][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.439][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:50:46.440][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-11-02 08:50:46.441][ef$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:46.443][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:46.444][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.446][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.447][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.449][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.450][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.451][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.453][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.454][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.455][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.457][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.458][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.460][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.461][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.462][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.464][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.465][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.466][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.468][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.469][ef$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:46.471][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:46.472][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.473][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.475][ef$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:46.476][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:46.477][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.479][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.480][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.482][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.483][ef$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.484][ef$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.486][private$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[2023-11-02 08:50:46.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:46.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:46.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:46.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:46.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-11-02 08:50:46.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-11-02 08:50:46.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-11-02 08:50:46.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.523][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.529][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.534][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-11-02 08:50:46.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.540][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.546][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.551][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-11-02 08:50:46.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-11-02 08:50:46.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.574][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:46.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:46.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.580][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:46.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:46.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.585][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-11-02 08:50:46.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-11-02 08:50:46.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:46.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:46.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.596][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:46.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:46.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-11-02 08:50:46.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-11-02 08:50:46.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.608][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.613][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.619][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-11-02 08:50:46.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-11-02 08:50:46.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-11-02 08:50:46.630][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2023-11-02 08:50:46.631][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-11-02 08:50:46.633][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-11-02 08:50:46.642][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-11-02 08:50:46.644][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-11-02 08:50:46.645][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-11-02 08:50:46.646][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-11-02 08:50:46.648][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-11-02 08:50:46.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-11-02 08:50:46.650][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-11-02 08:50:46.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-11-02 08:50:46.653][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-11-02 08:50:46.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 155 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_100_generic.R:16:1'): We can search for a compound ─────────────
Error in `if (!is.na(content) && cfg$isEnabled("cache.system") && !is.null(conn) && 
    cfg$get("cache.all.requests")) {
    logDebug("Saving content of request to cache.")
    cch$saveContentToFile(content, cache.id = conn$getCacheId(), 
        name = request.key, ext = "content")
    cch$saveContentToFile(request$toString(), cache.id = conn$getCacheId(), 
        name = request.key, ext = "request")
}`: missing value where TRUE/FALSE needed
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(db = `<LpdmpsSC>`, opt = `<named list>`)
 3.   └─db$searchCompound(...)
 4.     └─self$searchForEntries(fields, max.results = max.results)
 5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
 6.         └─self$wsLmsdSearch(...)
 7.           └─self$getBiodb()$getRequestScheduler()$sendRequest(request)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 155 ]
Error: Test failures
Execution halted

Example timings

biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings

nameusersystemelapsed
LipidmapsStructureConn1.0250.0835.146
LipidmapsStructureEntry0.2120.0000.213